[1] "ofn"        "-oTLUSC-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/LUSC-TP/22506957/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/22533933/transformed.cor.cli.txt"

nPatients in clinical file=504, in cluster file=501, common to both=501
[1]  82 501
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               91               410 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               91               410 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              202               299 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              202               299 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              223               278 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              223               278 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              143               358 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              143               358 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              108               393 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              108               393 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              315               186 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              315               186 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               31               470 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               31               470 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               480 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               480 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              309               192 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              309               192 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               97               404 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               97               404 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              108               393 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              108               393 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               92               409 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               92               409 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              238               263 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              238               263 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              220               281 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              220               281 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              129               372 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              129               372 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              256               245 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              256               245 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               62               439 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               62               439 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               91               410 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               91               410 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                78                423 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                78                423 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                44                457 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                44                457 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                75                426 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                75                426 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                89                412 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                89                412 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               226                275 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               226                275 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               151                350 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               151                350 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                39                462 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                39                462 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               126                375 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               126                375 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               107                394 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               107                394 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                86                415 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                86                415 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                85                416 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                85                416 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                65                436 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                65                436 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               158                343 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               158                343 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               148                353 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               148                353 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               102                399 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               102                399 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               115                386 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               115                386 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               163                338 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               163                338 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               263                238 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               263                238 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               251                250 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               251                250 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                57                444 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                57                444 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               222                279 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               222                279 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               64               437 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               64               437 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               79               422 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               79               422 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              155               346 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              155               346 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               60               441 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               60               441 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               477 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               477 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               44               457 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               44               457 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              310               191 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              310               191 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               73               428 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               73               428 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              315               186 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              315               186 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              297               204 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              297               204 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               79               422 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               79               422 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              290               211 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              290               211 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              114               387 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              114               387 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              114               387 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              114               387 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               60               441 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               60               441 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               50               451 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               50               451 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              243               258 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              243               258 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               54               447 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               54               447 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              315               186 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              315               186 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              247               254 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              247               254 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               215                286 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               215                286 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               229                272 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               229                272 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               169                332 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               169                332 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               143                358 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               143                358 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                39                462 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                39                462 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                47                454 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                47                454 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               311                190 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               311                190 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               167                334 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               167                334 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               141                360 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               141                360 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               163                338 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               163                338 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               184                317 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               184                317 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               292                209 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               292                209 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                91                410 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                91                410 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               141                360 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               141                360 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               190                311 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               190                311 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               162                339 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               162                339 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               110                391 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               110                391 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                459 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                459 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                49                452 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                49                452 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               264                237 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               264                237 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                98                403 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                98                403 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              145               356 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              145               356 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              114               387 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              114               387 
[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 501 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=202,	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=253,	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=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	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=21,	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=68,	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=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=105,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	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 501 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=45, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=10, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
112 294  71  24 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
112 294  71  24 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
112 294  71  24 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
112 294  71  24 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
317 133  40   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
317 133  40   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
317 133  40   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
317 133  40   5 
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=10, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=105, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=55, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    55  36
  1P GAIN WILD-TYPE 225 178
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               91               403 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               36               178 
$`1P GAIN MUTATED`
TCGA-33-4533 TCGA-43-2578 TCGA-56-8504 TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GB 
      133.74        22.49        16.77        66.61        20.78        30.81 
TCGA-90-7964 TCGA-94-7557 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-18-3414 TCGA-18-3415 
       14.07         0.16        19.10         0.07        23.54        92.15 
TCGA-21-1070 TCGA-21-1081 TCGA-21-1082 TCGA-21-5787 TCGA-22-1011 TCGA-22-1016 
      119.54         9.34       119.80        10.82         1.74        27.02 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-33-4582 TCGA-33-6738 TCGA-34-2608 
       71.34        79.20        18.84       103.53        63.35        32.88 
TCGA-34-5231 TCGA-34-5240 TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 
       65.23        50.66         1.12         4.04        33.90         4.01 
TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4141 TCGA-39-5021 TCGA-39-5022 
        0.39         8.12         7.46         0.39        68.58        55.20 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-3920 TCGA-43-6143 
       68.38        55.56        17.06        40.21        33.11        22.98 
TCGA-43-6770 TCGA-46-3765 TCGA-46-3769 TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 
       21.47        13.32         4.44        10.65         5.46        30.35 
TCGA-56-7223 TCGA-58-A46K TCGA-58-A46N TCGA-60-2695 TCGA-60-2708 TCGA-60-2719 
       14.53        34.36        29.92        21.11        80.45        42.64 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MS TCGA-63-A5MW 
       29.85        35.90        26.83        11.77        78.28        53.88 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2755 TCGA-66-2759 TCGA-66-2763 TCGA-66-2771 
       43.10        21.07         0.92        25.05         0.99        19.00 
TCGA-66-2782 TCGA-66-2783 TCGA-68-8251 TCGA-68-A59I TCGA-77-7138 TCGA-77-7338 
       12.00        24.95        13.35        16.18        11.18         0.16 
TCGA-77-8145 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7699 
        6.97        61.94        38.86        41.39         6.41        32.91 
TCGA-85-7844 TCGA-85-8072 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A512 
       29.95        30.64        19.86        30.48        27.16        15.29 
TCGA-90-A4ED TCGA-92-8064 TCGA-96-8169 TCGA-98-A538 TCGA-NC-A5HG TCGA-NC-A5HJ 
       20.22         5.26        18.31        27.16        64.54        13.74 
TCGA-NC-A5HN 
       49.28 

$`1P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 
       27.19        32.19        14.93        48.82        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
       22.06       129.01         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       31.27        17.88        18.38         7.76        78.18         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 
       11.61        12.03        19.99        13.05         3.45        17.00 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
       17.85        21.04         0.13         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-A5GA TCGA-90-7766 TCGA-94-7033 
       35.34        32.32         8.02        42.08         9.50        21.04 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
       18.38        16.14        57.07        19.36         2.76         5.69 
TCGA-98-A53D TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
       21.21        76.80        39.85        40.90        65.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 
        0.43         8.58        75.75       117.57        11.34        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 
       92.42        86.96         2.79       154.32        49.94        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       99.16        70.16        60.89        34.78        15.58        31.73 
TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
      122.43        43.23        31.63        88.11        41.69        33.93 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-4591 
       21.99         7.33         4.31        64.21        14.10        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       35.08        48.33        24.13         0.56        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       13.12        32.02        19.30         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 
       14.63        44.25         0.79        86.30        11.74        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        56.32        16.64        97.94        79.53       173.82 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      151.27        14.07        54.44         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
        6.94       110.99        44.19       118.36        27.16         2.63 
TCGA-34-2600 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 
       61.61        81.24        74.66         9.07        60.30        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-37-3789 
       44.75        39.32         4.96        38.79        26.43         0.43 
TCGA-37-4129 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN 
        7.96         7.82         6.81         3.39        37.58        21.70 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      133.25       126.58       111.35        82.52       102.18         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-43-2581 
       24.33         1.94        60.53        36.39        71.18        38.66 
TCGA-43-3394 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       39.12        27.91        24.89         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 
       13.38        11.77         9.73        14.20        12.16        13.02 
TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        9.83        13.91         0.39         0.39        29.95        28.34 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        8.75        27.45        28.96        12.43        18.25        21.90 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       18.48        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       17.49        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
        9.93        20.25        15.81        20.94        19.23        13.32 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.26        14.47         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
       29.95        71.24        16.47        34.78        85.12        56.65 
TCGA-58-A46M TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       35.24        12.23        10.22        96.82        37.94        92.71 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       21.93        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2720 TCGA-60-2724 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
        3.19        23.57        52.67        70.13        70.42        68.15 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
       55.30       102.67        70.62        58.65        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV 
       14.99        11.34        25.28        89.29        16.37        36.16 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       34.59        16.96         2.01         0.99         1.02         2.01 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
        0.99        43.99        21.01         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01         7.07        23.01         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
       12.03         3.98         1.97        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        4.04        22.98         5.03        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59J 
        4.01        49.05         2.73         6.64         6.94        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        29.56        73.12        75.09        23.28 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
      140.09         0.49        73.22        70.13       106.95        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       32.55         6.51        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       12.59        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       26.40        27.39        66.51        54.41        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       36.36       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       27.62         9.67        40.24        36.53        34.95        31.30 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1.38         1.15        18.94        25.15        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       31.56        26.79        34.52        10.09         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       22.45        16.77         5.29         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
       15.39         7.76        36.59        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR 
       22.59        30.28        34.13        30.97        24.36        19.73 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96        29.92        12.39         3.65 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       24.92         2.93        11.77        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        3.48         4.01         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       14.14        17.69        71.01        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.81        30.67        21.34        18.15         2.01        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       20.32        18.58        20.71        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK 
       13.41        11.84         4.54         1.22        57.30         4.21 
TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
        2.89        43.92        25.32        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
        3.65        33.07         3.72        12.72        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.07              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           133.74            173.82 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            23.54             21.34 
[1] "0.1 - 133.7 (23.5)" "0.0 - 173.8 (21.3)"
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         0       11       34        1         9        15
  1P GAIN WILD-TYPE       2       78      118        1        56        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  1P GAIN MUTATED           0         13          2        4
  1P GAIN WILD-TYPE         3         50         17        3
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                11                78
  STAGE IB                34               118
  STAGE II                 1                 1
  STAGE IIA                9                56
  STAGE IIB               15                80
  STAGE III                0                 3
  STAGE IIIA              13                50
  STAGE IIIB               2                17
  STAGE IV                 4                 3
[1] 10  2
[1] 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    17  57  12   5
  1P GAIN WILD-TYPE  95 237  59  19
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              17                95
  T2              57               237
  T3              12                59
  T4               5                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
  1P GAIN MUTATED    61  20   8   1
  1P GAIN WILD-TYPE 256 113  32   4
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              61               256
  N1              20               113
  N2               8                32
  N3               1                 4
[1] 4 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    79   4
  1P GAIN WILD-TYPE 332   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     79    4
  1P GAIN WILD-TYPE  332    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              79               332
  1               4                 3
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    22  69
  1P GAIN WILD-TYPE 108 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     22   69
  1P GAIN WILD-TYPE  108  302
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              22               108
  MALE                69               302
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    69  13
  1P GAIN WILD-TYPE 315  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     69   13
  1P GAIN WILD-TYPE  315   40
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               69               315
  YES              13                40
[1] 2 2
[1] FALSE
D1V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                       7
  1P GAIN WILD-TYPE                                     8
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  1P GAIN MUTATED                                        0
  1P GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                         0
  1P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                            84
  1P GAIN WILD-TYPE                                                         395
D1V10, multiclass
                                                             clus
vv                                                            1P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              84
                                                             clus
vv                                                            1P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               395
[1] 4 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    73   3   1   3
  1P GAIN WILD-TYPE 326   9   3  20
D1V13, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              73               326
  R1               3                 9
  R2               1                 3
  RX               3                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       2                         6    66
  1P GAIN WILD-TYPE     7                        25   283
D1V14, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               6                25
  WHITE                                  66               283
[1] 3 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  64
  1P GAIN WILD-TYPE   7 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   64
  1P GAIN WILD-TYPE    7  253
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              64               253
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   111  87
  1Q GAIN WILD-TYPE 169 127
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              198               296 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               87               127 
$`1Q GAIN MUTATED`
TCGA-18-3406 TCGA-22-1017 TCGA-22-A5C4 TCGA-33-4533 TCGA-43-2578 TCGA-43-7657 
       12.20        48.82        22.06       133.74        22.49         7.76 
TCGA-56-8305 TCGA-56-8504 TCGA-56-A5DR TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GA 
        3.45        16.77         0.13        66.61        20.78        42.08 
TCGA-77-A5GB TCGA-90-7964 TCGA-94-7557 TCGA-94-7943 TCGA-J1-A4AH TCGA-NC-A5HD 
       30.81        14.07         0.16        18.38        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 
       76.80        40.90         0.43        75.75       117.57        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
       92.15        36.07        49.94       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 TCGA-21-5787 
       70.16        34.78         9.34       119.80        41.69        10.82 
TCGA-22-0940 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
       21.99         1.74        14.10        27.02        20.48        48.33 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 
        0.56        38.17        19.30        63.55        14.63        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4538 
       71.34        79.20        18.84        30.12        62.86        97.94 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
      173.82       103.53       151.27        14.07        54.44        63.35 
TCGA-33-A4WN TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
        4.70       110.99        44.19         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 
       65.23        60.30        50.66        39.32         1.12         4.04 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 
       33.90         4.01         0.39         7.46         7.82         0.39 
TCGA-37-A5EN TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5035 TCGA-39-5037 
       21.70       126.58        68.58        55.20        68.38        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 
       17.06        40.21        38.66        33.11        22.98        21.47 
TCGA-43-A475 TCGA-46-3765 TCGA-46-3769 TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 
        9.73        13.32         4.44        10.65         0.39        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-56-7223 TCGA-56-7582 TCGA-56-8622 TCGA-56-A4BX 
        5.46        30.35        14.53        19.76         1.81        13.32 
TCGA-58-8388 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       13.55        34.78        34.36        35.24        29.92        21.11 
TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       10.22        21.93        80.45        29.85        35.90        26.83 
TCGA-60-2726 TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-63-A5MW TCGA-66-2734 
       11.77        59.97        45.57        78.28        53.88        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 
        2.01        21.07         0.92         0.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 
        0.99        23.01        19.00         3.02         2.01         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-68-8251 TCGA-68-A59I 
       12.00        24.95         1.97        40.01        13.35        16.18 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       14.73        73.12        23.28        11.18       140.09         0.49 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8145 
        0.16        46.78        32.55        86.76        55.73         6.97 
TCGA-77-8156 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
       36.36        61.94        27.62        38.86        41.39         6.41 
TCGA-85-7696 TCGA-85-7699 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
       36.53        32.91        29.95        25.15        19.04        24.13 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
       31.56        30.64        10.09        16.77         5.29         3.09 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M 
       18.08        22.59        30.28        19.86        30.48        27.16 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE 
       14.96        15.29         3.65         2.93        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-A4VJ TCGA-94-A5I6 
       10.59         2.70         3.48         5.26        14.14        17.69 
TCGA-96-8169 TCGA-96-A4JL TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 
       18.31        27.68        27.16        18.58        20.71        16.11 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HP 
       13.41        11.84        64.54        13.74        49.28        25.32 

$`1Q GAIN WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
        4.47       123.19         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4589 
       32.19        14.93        60.66        64.93       129.01         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 
       19.76        31.50        28.96        31.27        17.88        18.38 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 
       78.18         2.93        11.61        12.03        19.99        13.05 
TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
       17.00        17.85        21.04         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-90-7766 TCGA-94-7033 TCGA-94-A5I4 
       35.34        32.32         8.02         9.50        21.04        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HM 
       57.07        19.36         2.76         5.69        21.21        39.85 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3412 TCGA-18-3419 TCGA-18-3421 
       65.65        16.80         8.58        11.34        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2.79       154.32        60.89        15.58        31.73       122.43 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-22-0944 TCGA-22-1002 
       43.23        31.63        88.11        33.93         7.33         4.31 
TCGA-22-1005 TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       64.21        35.08        24.13        34.75        13.12        32.02 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5491 
        9.57        11.77        44.25         0.79        11.74        56.32 
TCGA-22-5492 TCGA-33-4547 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ 
       16.64        79.53         0.30        36.62         6.94       118.36 
TCGA-33-AASL TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 
       27.16        81.24        74.66         9.07        16.93        44.75 
TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
        4.96        38.79        26.43         0.43         7.96         8.12 
TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5019 TCGA-39-5024 
        6.81         3.39        37.58       133.25       111.35        82.52 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
      102.18         1.71        24.33         1.94        60.53        36.39 
TCGA-39-5036 TCGA-43-3394 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 
       71.18        39.12        27.91        24.89         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 
       19.59        13.38        11.77        14.20        12.16        13.02 
TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7811 TCGA-52-7812 
        9.83        13.91         0.39        29.95         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 
       28.96        12.43        18.25        21.90        18.48        31.27 
TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       30.41         6.51         0.10        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 
        4.93         3.48        26.89        14.07         1.35        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
       13.81        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       19.23        18.74         0.26        14.47         0.03        13.25 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-60-2697 
       29.95        71.24        16.47        85.12        56.65        12.23 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       96.82        37.94        92.71        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2724 TCGA-63-6202 
       50.33        48.49        42.64         3.19        23.57        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG 
       70.13        70.42        68.15        55.30       102.67        70.62 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT 
       58.65        14.99        11.34        25.28        89.29        16.37 
TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       36.16        34.59        16.96         0.99         1.02         2.01 
TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       43.99         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       19.00        12.03        25.97        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 
        2.73         6.64         6.94        12.07        12.33        29.56 
TCGA-77-6844 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8007 TCGA-77-8128 
       75.09        73.22        70.13       106.95         6.51        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
      156.66        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       11.54        26.40        27.39        66.51        54.41        65.49 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       60.53       126.18       132.36       150.25        22.29         5.92 
TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 
        9.67        40.24        34.95        31.30         1.38         1.15 
TCGA-85-7950 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       18.94        26.79        34.52         0.76        13.22        22.45 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       32.71         2.01        15.39         7.76        36.59        38.14 
TCGA-85-8584 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z 
       12.59        34.13        30.97        24.36        19.73        16.21 
TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 TCGA-92-8063 
       15.85        29.92        12.39        24.92        11.77         4.01 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-8170 
        2.30         4.01         5.03        26.63        71.01        17.46 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B 
       21.44        30.81        30.67        21.34        18.15         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HH 
       27.02        20.32        12.89        13.18         4.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT 
       57.30         4.21         2.89        43.92        14.73        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       83.57         3.65        33.07         3.72        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.07              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           173.82            156.66 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            22.80             20.63 
[1] "0.1 - 173.8 (22.8)" "0.0 - 156.7 (20.6)"
[1] "hr=" "1"  
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         0       27       72        1        23        39
  1Q GAIN WILD-TYPE       2       62       80        1        42        56
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  1Q GAIN MUTATED           0         25          6        6
  1Q GAIN WILD-TYPE         3         38         13        1
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                27                62
  STAGE IB                72                80
  STAGE II                 1                 1
  STAGE IIA               23                42
  STAGE IIB               39                56
  STAGE III                0                 3
  STAGE IIIA              25                38
  STAGE IIIB               6                13
  STAGE IV                 6                 1
[1] 10  2
[1] 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    35 130  26  11
  1Q GAIN WILD-TYPE  77 164  45  13
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              35                77
  T2             130               164
  T3              26                45
  T4              11                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
  1Q GAIN MUTATED   127  57  15   1
  1Q GAIN WILD-TYPE 190  76  25   4
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0             127               190
  N1              57                76
  N2              15                25
  N3               1                 4
[1] 4 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   171   6
  1Q GAIN WILD-TYPE 240   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    171    6
  1Q GAIN WILD-TYPE  240    1
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             171               240
  1               6                 1
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    46 156
  1Q GAIN WILD-TYPE  84 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     46  156
  1Q GAIN WILD-TYPE   84  215
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              46                84
  MALE               156               215
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   154  22
  1Q GAIN WILD-TYPE 230  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    154   22
  1Q GAIN WILD-TYPE  230   31
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              154               230
  YES              22                31
[1] 2 2
[1] FALSE
D2V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                      11
  1Q GAIN WILD-TYPE                                     4
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  1Q GAIN MUTATED                                        0
  1Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                         1
  1Q GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                           190
  1Q GAIN WILD-TYPE                                                         289
D2V10, multiclass
                                                             clus
vv                                                            1Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             190
                                                             clus
vv                                                            1Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D2V11, continuous
D2V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED   167   5   1   9
  1Q GAIN WILD-TYPE 232   7   3  14
D2V13, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             167               232
  R1               5                 7
  R2               1                 3
  RX               9                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       3                        11   146
  1Q GAIN WILD-TYPE     6                        20   203
D2V14, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              11                20
  WHITE                                 146               203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     4 128
  1Q GAIN WILD-TYPE   4 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4  128
  1Q GAIN WILD-TYPE    4  189
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO             128               189
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED   131  89
  2P GAIN WILD-TYPE 149 125
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              220               274 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               89               125 
$`2P GAIN MUTATED`
TCGA-18-3409 TCGA-21-A5DI TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-34-2604 
      123.19        32.19        60.66        22.06       129.01        31.50 
TCGA-34-2605 TCGA-43-5668 TCGA-43-7658 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 
       28.96        18.38        78.18        13.05         3.45        17.00 
TCGA-56-8504 TCGA-56-A4BY TCGA-60-2711 TCGA-60-2712 TCGA-63-A5MH TCGA-77-A5GA 
       16.77        17.85        41.42         9.01        66.61        42.08 
TCGA-90-7964 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       14.07         0.16        18.38        16.14        57.07        19.36 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 
       19.10         0.07         0.43         8.58       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-21-1072 TCGA-21-1076 
       23.54        92.15        36.07        92.42        99.16        60.89 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-22-4591 
       31.73         9.34        43.23        88.11        33.93        20.48 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-5473 TCGA-22-5474 
       24.13        38.17        13.12        32.02        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 
       44.25         0.79        86.30        71.34        18.84        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-6738 
       56.32        16.64       173.82       103.53       151.27        63.35 
TCGA-33-A4WN TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 
        4.70       110.99       118.36         2.63        61.61        65.23 
TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 
        9.07        50.66        16.93        39.32         1.12        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 
        4.04        26.43        33.90         0.39         8.12         7.82 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 
       37.58        21.70       133.25       126.58       111.35       102.18 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
       68.38        71.18        55.56        17.06        40.21        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-8115 TCGA-46-3765 
       39.12        33.11        27.91        22.98        13.38        13.32 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-51-4080 TCGA-52-7809 
       13.02         9.83         4.44        10.65         0.39         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       30.35         8.75        18.25        18.48        14.53        31.27 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
       19.76         6.51         3.48        20.25        15.81        19.23 
TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L 
       13.32         0.26        71.24        16.47        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 TCGA-60-2719 
       35.24        29.92        10.22        96.82        80.45        42.64 
TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI 
       23.57        11.77        52.67        55.30       102.67        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV 
       59.97        45.57        25.28        89.29        78.28        36.16 
TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 
        2.01        21.01        25.05         2.01        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2787 TCGA-66-2789 TCGA-66-2792 TCGA-66-2793 
        3.02         2.01        40.01         4.04        30.02        10.06 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I TCGA-70-6722 
        4.01        49.05         2.73         6.64        16.18        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       12.33        29.56        23.28        11.18       140.09         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8009 TCGA-77-8130 TCGA-77-8136 
       73.22        70.13       106.95        55.73       156.66        39.09 
TCGA-77-8139 TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G8 
      104.09        66.51        54.41        36.36       132.36        61.94 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86         9.67        41.39         6.41        36.53 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 
        1.15        29.95        24.13        31.56        30.64        10.09 
TCGA-85-8350 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       22.45        32.71        18.08        22.59        34.13        30.97 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7767 
       19.73        27.16        15.85        14.96         3.65         2.93 
TCGA-90-7769 TCGA-90-A4EE TCGA-92-7341 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
       11.77        22.62         3.48         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-8169 TCGA-98-7454 TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J 
       17.69        18.31        21.44        27.16        18.58        20.71 
TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HL 
       16.11        11.84        64.54         1.22         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-O2-A52V TCGA-XC-AA0X 
       49.28        14.73        43.89         0.20 

$`2P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 
       14.93        48.82        64.93       133.74         1.55        19.76 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 
       31.27        17.88        22.49         7.76         2.93        11.61 
TCGA-43-A56V TCGA-56-7221 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2715 
       12.03        19.99        21.04         0.13         3.58        35.34 
TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 TCGA-94-7033 
       32.32         8.02        20.78        30.81         9.50        21.04 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
        2.76         5.69        21.21        76.80        39.85        40.90 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       65.65        16.80        75.75        86.96         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
       49.94       119.54        46.88        70.16        34.78        15.58 
TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 
      122.43       119.80        31.63        41.69        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        7.33         4.31        64.21         1.74        14.10        27.02 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 
       35.08        48.33         0.56        34.75        19.30         9.57 
TCGA-22-4613 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-33-4538 TCGA-33-4547 
       11.77        79.20        11.74        30.12        97.94        79.53 
TCGA-33-4586 TCGA-33-4587 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI 
       14.07        54.44         0.30        36.62         6.94        44.19 
TCGA-33-AASL TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 
       27.16        32.88        81.24        74.66        60.30        44.75 
TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 
        4.96         4.01         0.43         7.96         7.46         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
        0.39         3.39        68.58        55.20        82.52         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-43-6647 TCGA-43-6770 
       24.33         1.94        60.53        36.39        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        5.46         3.81        19.59        11.77         9.73        14.20 
TCGA-46-3766 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 
       12.16        13.91         0.39        29.95        28.34        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 
       28.96        12.43        21.90        30.41         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       33.24        14.96         4.93        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-A49D 
        1.81        22.75        13.81        10.36         9.93        20.94 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       18.74        14.47         0.03        13.25        13.55        29.95 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2695 TCGA-60-2697 TCGA-60-2704 TCGA-60-2706 
       34.78        85.12        21.11        12.23        37.94        92.71 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       21.93        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 
        3.19        29.85        35.90        26.83        70.13        70.42 
TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MT TCGA-63-A5MW 
       68.15        70.62        14.99        11.34        16.37        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       34.59        16.96        43.10        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 
        2.01         0.92         0.99        43.99         0.99         2.01 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        1.02         2.01         7.07        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 
       12.00        24.95         1.97        25.97        22.98        22.98 
TCGA-66-2791 TCGA-66-2794 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6843 
        5.03        54.08         6.94        13.35        14.73        73.12 
TCGA-77-6844 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
       75.09         0.16        46.78        32.55         6.51        86.76 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 
       37.81        12.59        53.92        17.72        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 
       27.39         6.97        65.49        60.53       126.18       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       22.29         5.92        40.24        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8276 
        1.38        18.94        25.15        19.04        26.79        34.52 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 
        0.76        13.22        16.77         5.29         3.09         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL 
       15.39         7.76        36.59        38.14        12.59        30.28 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 
       19.86        24.36        30.48        16.21        15.29        29.92 
TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
       12.39        24.92        20.22        10.59         2.70         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL 
        5.26         2.30         4.01        71.01        17.46        27.68 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.81        30.67        21.34        18.15         2.01        27.02 
TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HI 
       20.32        12.89        13.18        13.41         4.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
       13.74        43.92        25.32        26.43        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB 
       33.07         3.72        12.72        11.18 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           173.82            154.32 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            24.13             20.27 
[1] "0.1 - 173.8 (24.1)" "0.0 - 154.3 (20.3)"
[1] "hr=" "1.5"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         1       33       62        2        32        48
  2P GAIN WILD-TYPE       1       56       90        0        33        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  2P GAIN MUTATED           0         30         10        3
  2P GAIN WILD-TYPE         3         33          9        4
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                33                56
  STAGE IB                62                90
  STAGE II                 2                 0
  STAGE IIA               32                33
  STAGE IIB               48                47
  STAGE III                0                 3
  STAGE IIIA              30                33
  STAGE IIIB              10                 9
  STAGE IV                 3                 4
[1] 10  2
[1] 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    42 130  38  13
  2P GAIN WILD-TYPE  70 164  33  11
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              42                70
  T2             130               164
  T3              38                33
  T4              13                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
  2P GAIN MUTATED   133  70  17   2
  2P GAIN WILD-TYPE 184  63  23   3
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0             133               184
  N1              70                63
  N2              17                23
  N3               2                 3
[1] 4 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   189   3
  2P GAIN WILD-TYPE 222   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    189    3
  2P GAIN WILD-TYPE  222    4
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0             189               222
  1               3                 4
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    43 180
  2P GAIN WILD-TYPE  87 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     43  180
  2P GAIN WILD-TYPE   87  191
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              43                87
  MALE               180               191
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   166  30
  2P GAIN WILD-TYPE 218  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    166   30
  2P GAIN WILD-TYPE  218   23
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO              166               218
  YES              30                23
[1] 2 2
[1] FALSE
D3V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                      11
  2P GAIN WILD-TYPE                                     4
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  2P GAIN MUTATED                                        1
  2P GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                         0
  2P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                           211
  2P GAIN WILD-TYPE                                                         268
D3V10, multiclass
                                                             clus
vv                                                            2P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             211
                                                             clus
vv                                                            2P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               268
[1] 4 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   182   3   1   8
  2P GAIN WILD-TYPE 217   9   3  15
D3V13, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0             182               217
  R1               3                 9
  R2               1                 3
  RX               8                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       4                        10   162
  2P GAIN WILD-TYPE     5                        21   187
D3V14, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              10                21
  WHITE                                 162               187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1 142
  2P GAIN WILD-TYPE   7 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1  142
  2P GAIN WILD-TYPE    7  175
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO             142               175
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    80  60
  2Q GAIN WILD-TYPE 200 154
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              140               354 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               60               154 
$`2Q GAIN MUTATED`
TCGA-18-3409 TCGA-21-A5DI TCGA-33-4532 TCGA-34-2604 TCGA-34-2605 TCGA-43-5668 
      123.19        32.19       129.01        31.50        28.96        18.38 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-60-2711 TCGA-60-2712 
       13.05         3.45        17.00        16.77        41.42         9.01 
TCGA-77-A5GA TCGA-90-7964 TCGA-94-7557 TCGA-96-7545 TCGA-J1-A4AH TCGA-NC-A5HD 
       42.08        14.07         0.16        57.07        19.10         0.07 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-21-1072 
        0.43         8.58       117.57        11.34        23.54        99.16 
TCGA-21-1081 TCGA-21-1083 TCGA-22-4595 TCGA-22-4605 TCGA-22-5474 TCGA-22-5477 
        9.34        43.23        24.13        32.02        14.63        44.25 
TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4566 
       71.34        18.84        62.86        56.32        16.64       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 TCGA-33-AASD TCGA-34-2596 
      103.53       151.27        54.44        63.35       110.99         2.63 
TCGA-34-2600 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 
       61.61         9.07        50.66        16.93        39.32         1.12 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4133 TCGA-39-5011 TCGA-39-5016 
        4.04        33.90         0.39         7.82       133.25       126.58 
TCGA-39-5019 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
      111.35        68.38        71.18        55.56        17.06        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-46-3768 
       38.66        39.12        33.11        27.91        22.98         9.83 
TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-5898 TCGA-56-7222 
        0.39         5.46        30.35         8.75        18.25        18.48 
TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8391 
       14.53        19.76         6.51        13.32         0.26        71.24 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-60-2708 TCGA-60-2719 TCGA-60-2726 
       35.24        29.92        96.82        80.45        42.64        11.77 
TCGA-63-6202 TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MR TCGA-63-A5MS TCGA-66-2759 
       52.67        58.65        59.97        89.29        78.28        25.05 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2792 TCGA-66-2793 TCGA-68-7755 
       23.01         3.02         2.01        30.02        10.06         2.73 
TCGA-68-7756 TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 TCGA-77-7142 
        6.64        12.33        29.56        23.28       140.09        73.22 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8139 TCGA-77-8145 TCGA-77-8150 TCGA-77-8156 
       55.73       156.66       104.09         6.97        54.41        36.36 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
      132.36       150.25        61.94        38.86         9.67        41.39 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8070 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
        1.15        29.95        31.56        10.09         0.76        22.45 
TCGA-85-8354 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 
       32.71        22.59        34.13        19.73        27.16        15.85 
TCGA-85-A511 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7341 TCGA-94-8490 TCGA-94-A5I6 
       14.96        11.77        22.62         3.48         5.03        17.69 
TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HK 
       27.16        18.58        20.71        11.84        64.54         4.21 
TCGA-NC-A5HL TCGA-NC-A5HN 
        2.89        49.28 

$`2Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 
       14.93        48.82        60.66        64.93        22.06       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-7657 
        1.55        19.76        31.27        17.88        22.49         7.76 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-A4BY 
       78.18         2.93        11.61        12.03        19.99        17.85 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
       21.04         0.13         3.58        35.34        32.32        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 TCGA-94-7033 TCGA-94-7943 
        8.02        20.78        30.81         9.50        21.04        18.38 
TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HE 
       16.14        19.36         2.76         5.69        21.21        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3415 
       39.85        40.90        65.65        16.80        75.75        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       36.07        92.42        86.96         2.79       154.32        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
      119.54        46.88        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
       31.73       122.43       119.80        31.63        88.11        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       33.93        10.82        21.99         7.33         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
        1.74        14.10        27.02        20.48        35.08        48.33 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 
        0.56        38.17        34.75        13.12        19.30         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 
       11.77        63.55         0.79        86.30        79.20        11.74 
TCGA-22-5485 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW 
       30.12        97.94        79.53        14.07         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2608 
       36.62         6.94        44.19       118.36        27.16        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5929 
       65.23        81.24        74.66        60.30        44.75         4.96 
TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
       38.79        26.43         4.01         0.43         7.96         8.12 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN 
        7.46         6.81         0.39         3.39        37.58        21.70 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1.94        60.53        36.39        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        3.81        19.59        13.38        11.77         9.73        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       13.32        12.16        13.02         4.44        10.65        13.91 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        0.39        29.95        28.34        27.45        28.96        12.43 
TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       21.90        31.27        30.41         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       14.96         4.93         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75        13.81        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 
       15.81        20.94        19.23        18.74        14.47         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       13.25        13.55        29.95        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 
       34.36        56.65        21.11        12.23        10.22        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       92.71        21.93        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       48.49         3.19        29.85        35.90        23.57        26.83 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG 
       70.13        70.42        68.15        55.30       102.67        70.62 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MV 
       45.57        14.99        11.34        25.28        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       53.88        34.59        16.96        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        0.99         1.02         2.01         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       21.01         0.99         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        7.07        19.00        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       24.95         1.97        25.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 
       22.98         5.03        54.08         4.01        49.05         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 
       13.35        16.18        14.73        12.07        73.12        75.09 
TCGA-77-7138 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
       11.18         0.49        70.13       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
       32.55         6.51        86.76        37.81        12.59        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 
       39.09        17.72        11.54        26.40        27.39        66.51 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF 
       65.49        60.53       126.18        22.29         5.92        27.62 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       40.24         6.41        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
        1.38        18.94        25.15        19.04        24.13        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
       30.64        34.52        13.22        16.77         5.29         3.09 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01        15.39         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       18.08        30.28        30.97        19.86        24.36        30.48 
TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       16.21        15.29        29.92        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 
        2.93        20.22        10.59         2.70         4.01         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        2.30         4.01        26.63        14.14        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44        30.81        30.67        21.34 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 TCGA-L3-A524 
       18.15         2.01        27.02        20.32        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       13.18        13.41         4.54         1.22        57.30        13.74 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
       43.92        25.32        14.73        26.43        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         3.72        12.72        43.89        11.18         0.20 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           173.82            154.32 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           27.160            20.975 
[1] "0.1 - 173.8 (27.2)" "0.0 - 154.3 (21.0)"
[1] "hr=" "1.4"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         1       17       45        1        20        34
  2Q GAIN WILD-TYPE       1       72      107        1        45        61
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  2Q GAIN MUTATED           0         18          5        2
  2Q GAIN WILD-TYPE         3         45         14        5
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                17                72
  STAGE IB                45               107
  STAGE II                 1                 1
  STAGE IIA               20                45
  STAGE IIB               34                61
  STAGE III                0                 3
  STAGE IIIA              18                45
  STAGE IIIB               5                14
  STAGE IV                 2                 5
[1] 10  2
[1] 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    24  88  22   9
  2Q GAIN WILD-TYPE  88 206  49  15
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              24                88
  T2              88               206
  T3              22                49
  T4               9                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
  2Q GAIN MUTATED    89  43  11   0
  2Q GAIN WILD-TYPE 228  90  29   5
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              89               228
  N1              43                90
  N2              11                29
  N3               0                 5
[1] 4 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   119   2
  2Q GAIN WILD-TYPE 292   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED    119    2
  2Q GAIN WILD-TYPE  292    5
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0             119               292
  1               2                 5
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    28 115
  2Q GAIN WILD-TYPE 102 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     28  115
  2Q GAIN WILD-TYPE  102  256
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              28               102
  MALE               115               256
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED   109  19
  2Q GAIN WILD-TYPE 275  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED    109   19
  2Q GAIN WILD-TYPE  275   34
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO              109               275
  YES              19                34
[1] 2 2
[1] FALSE
D4V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED                                       8
  2Q GAIN WILD-TYPE                                     7
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  2Q GAIN MUTATED                                        1
  2Q GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED                                         1
  2Q GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                           133
  2Q GAIN WILD-TYPE                                                         346
D4V10, multiclass
                                                             clus
vv                                                            2Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             133
                                                             clus
vv                                                            2Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D4V11, continuous
D4V12, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED   116   3   0   4
  2Q GAIN WILD-TYPE 283   9   4  19
D4V13, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0             116               283
  R1               3                 9
  R2               0                 4
  RX               4                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       3                         7   107
  2Q GAIN WILD-TYPE     6                        24   242
D4V14, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               7                24
  WHITE                                 107               242
[1] 3 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     1  97
  2Q GAIN WILD-TYPE   7 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   97
  2Q GAIN WILD-TYPE    7  220
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              97               220
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    54  53
  3P GAIN WILD-TYPE 226 161
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              107               387 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               53               161 
$`3P GAIN MUTATED`
TCGA-18-3410 TCGA-22-1000 TCGA-33-4533 TCGA-34-2609 TCGA-43-A56V TCGA-56-8305 
        4.80        14.93       133.74        31.27        12.03         3.45 
TCGA-56-8308 TCGA-56-A5DR TCGA-60-2715 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       17.00         0.13        35.34        20.78        42.08        30.81 
TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 TCGA-98-8020 TCGA-J1-A4AH TCGA-NC-A5HR 
       21.04        18.38        57.07         2.76        19.10        40.90 
TCGA-21-1080 TCGA-21-1081 TCGA-22-1002 TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 
      122.43         9.34         4.31        35.08        24.13        34.75 
TCGA-22-5477 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4582 
       44.25        30.12        62.86        56.32        97.94       103.53 
TCGA-33-4586 TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-34-5232 TCGA-34-5236 
       14.07         0.30         6.94       110.99        81.24         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-37-3783 TCGA-37-4133 
       50.66        16.93        39.32         1.12         4.01         7.82 
TCGA-37-A5EL TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5029 TCGA-39-5030 
       37.58       111.35        68.58        55.20        24.33         1.94 
TCGA-39-5037 TCGA-39-5040 TCGA-43-3394 TCGA-43-5670 TCGA-43-6771 TCGA-46-3766 
       55.56        17.06        39.12        27.91         5.46        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-52-7810 
       13.02         9.83         4.44        10.65        13.91        30.35 
TCGA-56-5898 TCGA-56-7223 TCGA-56-7730 TCGA-56-8083 TCGA-56-A49D TCGA-56-A4ZK 
       18.25        14.53         6.51         4.93        20.94        18.74 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46M TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       34.78        85.12        35.24        96.82        37.94        92.71 
TCGA-60-2713 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MP TCGA-63-A5MV TCGA-66-2727 
       56.91        68.15       102.67        25.28        36.16        16.96 
TCGA-66-2756 TCGA-66-2766 TCGA-66-2771 TCGA-66-2777 TCGA-70-6722 TCGA-77-8008 
        0.99         1.02        19.00         2.01        12.07        86.76 
TCGA-77-8009 TCGA-77-8136 TCGA-77-8145 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G8 
       55.73        39.09         6.97        54.41       132.36        61.94 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-8049 TCGA-85-8350 
       27.62        40.24         6.41        36.53        19.04        22.45 
TCGA-85-8352 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4JC TCGA-94-8035 
        5.29        36.59        38.14        18.08        19.86         4.01 
TCGA-98-A538 TCGA-98-A53B TCGA-NC-A5HK TCGA-O2-A52N TCGA-XC-AA0X 
       27.16         2.01         4.21        33.07         0.20 

$`3P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       32.19        48.82        60.66        64.93        22.06       129.01 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 
        1.55        19.76        31.50        28.96        17.88        22.49 
TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 
       18.38         7.76        78.18         2.93        11.61        19.99 
TCGA-56-8201 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 
       13.05        16.77        17.85        21.04         3.58        41.42 
TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-90-7766 TCGA-90-7964 
        9.01        32.32        66.61         8.02         9.50        14.07 
TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD 
        0.16        16.14        19.36         5.69        21.21         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
       76.80        39.85        65.65        16.80         0.43         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
       75.75       117.57        11.34        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.42        86.96         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       46.88        99.16        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
       31.73       119.80        43.23        31.63        88.11        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 
       33.93        10.82        21.99         7.33        64.21         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       14.10        27.02        20.48        48.33         0.56        38.17 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       13.12        32.02        19.30         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
       14.63         0.79        86.30        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 
       18.84        16.64        79.53       173.82       151.27        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
       63.35         4.70        36.62        44.19       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 
        2.63        61.61        32.88        65.23        74.66        60.30 
TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       44.75         4.96        38.79         4.04        26.43        33.90 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
        0.43         0.39         7.96         8.12         7.46         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 
        0.39         3.39        21.70       133.25       126.58        82.52 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
      102.18         1.71        60.53        36.39        68.38        71.18 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       40.21        38.66        33.11        22.98        24.89        21.47 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        3.81        19.59        13.38        11.77         9.73        14.20 
TCGA-46-3765 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       13.32         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 
        8.75        27.45        28.96        12.43        21.90        18.48 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       31.27        30.41        19.76         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
       14.96         3.48        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       19.23        13.32         0.26        14.47         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L 
       13.55        29.95        71.24        16.47        34.36        56.65 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 
       29.92        21.11        12.23        10.22        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       49.48        66.54        50.33        48.49        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       29.85        35.90        23.57        26.83        11.77        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       70.13        70.42        55.30        70.62        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       45.57        14.99        11.34        89.29        78.28        16.37 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       53.88        34.59        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        1.02         2.01         0.92        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
        0.99         2.01         2.01         2.01         7.07        23.01 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        3.02        19.00        12.03         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1.97        25.97        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         6.94        13.35        16.18        14.73 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.33        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
       46.78        32.55         6.51        37.81       156.66        12.59 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       53.92        17.72       104.09        11.54        26.40        27.39 
TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 
       66.51        65.49        60.53        36.36       126.18       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 
       22.29         5.92        38.86         9.67        41.39        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
       31.30        32.91         1.38         1.15        29.95        18.94 
TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       25.15        24.13        31.56        26.79        30.64        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
       10.09         0.76        13.22        16.77         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL 
        2.01        15.39         7.76        12.59        22.59        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       34.13        30.97        24.36        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       16.21        15.85        14.96        15.29        29.92        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
        3.65        24.92         2.93        11.77        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       10.59         2.70         3.48         4.01         5.26         2.30 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        5.03        26.63        14.14        17.69        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44        30.81        30.67        21.34 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       18.15        27.02        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG 
       16.11        13.18        13.41        11.84         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO 
        1.22        57.30        13.74         2.89        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q 
       25.32        14.73        26.43        83.57         3.65         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       12.72        43.89        11.18 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.13              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           133.74            173.82 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            24.13             21.47 
[1] "0.1 - 133.7 (24.1)" "0.0 - 173.8 (21.5)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         1       20       26        1        11        26
  3P GAIN WILD-TYPE       1       69      126        1        54        69
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  3P GAIN MUTATED           0         20          2        0
  3P GAIN WILD-TYPE         3         43         17        7
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                20                69
  STAGE IB                26               126
  STAGE II                 1                 1
  STAGE IIA               11                54
  STAGE IIB               26                69
  STAGE III                0                 3
  STAGE IIIA              20                43
  STAGE IIIB               2                17
  STAGE IV                 0                 7
[1] 10  2
[1] 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    24  61  18   5
  3P GAIN WILD-TYPE  88 233  53  19
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              24                88
  T2              61               233
  T3              18                53
  T4               5                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
  3P GAIN MUTATED    64  30  11   0
  3P GAIN WILD-TYPE 253 103  29   5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              64               253
  N1              30               103
  N2              11                29
  N3               0                 5
[1] 4 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    92   0
  3P GAIN WILD-TYPE 319   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     92    0
  3P GAIN WILD-TYPE  319    7
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              92               319
  1               0                 7
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    21  87
  3P GAIN WILD-TYPE 109 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     21   87
  3P GAIN WILD-TYPE  109  284
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              21               109
  MALE                87               284
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    77  17
  3P GAIN WILD-TYPE 307  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     77   17
  3P GAIN WILD-TYPE  307   36
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               77               307
  YES              17                36
[1] 2 2
[1] FALSE
D5V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                       2
  3P GAIN WILD-TYPE                                    13
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  3P GAIN MUTATED                                        0
  3P GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                         0
  3P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                           106
  3P GAIN WILD-TYPE                                                         373
D5V10, multiclass
                                                             clus
vv                                                            3P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             106
                                                             clus
vv                                                            3P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
D5V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    83   5   1   5
  3P GAIN WILD-TYPE 316   7   3  18
D5V13, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              83               316
  R1               5                 7
  R2               1                 3
  RX               5                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       2                         9    76
  3P GAIN WILD-TYPE     7                        22   273
D5V14, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               9                22
  WHITE                                  76               273
[1] 3 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  72
  3P GAIN WILD-TYPE   6 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   72
  3P GAIN WILD-TYPE    6  245
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              72               245
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   176 136
  3Q GAIN WILD-TYPE 104  78
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              312               182 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              136                78 
$`3Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
        4.47       123.19         4.80        27.19        32.19        14.93 
TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 TCGA-34-2609 
       64.93       129.01       133.74         1.55        31.50        31.27 
TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56V TCGA-56-8305 
       22.49         7.76        78.18         2.93        12.03         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2712 
       17.00        16.77        17.85        21.04         0.13         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
       35.34        32.32        66.61         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 
       30.81         9.50        14.07        21.04        18.38        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR 
       19.36         2.76        19.10         0.07        39.85        40.90 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
        0.43         8.58        23.54        36.07        92.42        86.96 
TCGA-18-4086 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 
        2.79       119.54        46.88        60.89        34.78       122.43 
TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
        9.34        43.23        31.63        88.11        41.69        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
       10.82        21.99         4.31        14.10        20.48        35.08 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       24.13        38.17        34.75        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5485 TCGA-22-5489 
       11.77        44.25        86.30        71.34        30.12        62.86 
TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
       56.32        97.94        79.53       173.82       103.53        14.07 
TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
       54.44         4.70         0.30         6.94       110.99        44.19 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5236 
       27.16         2.63        61.61        32.88        81.24         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 
       50.66        16.93        44.75        39.32         1.12         4.04 
TCGA-37-3783 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        4.01         8.12         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-37-A5EL TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        3.39        37.58       126.58       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 
       82.52         1.71        24.33         1.94        60.53        68.38 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       55.56        17.06        40.21        39.12        33.11        27.91 
TCGA-43-6143 TCGA-43-6771 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       22.98         5.46        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 
        4.44        10.65        13.91         0.39        29.95         5.46 
TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 
       30.35        12.43        18.25        14.53        30.41         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 
        0.10        17.49        14.96         4.93         3.48        14.07 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
       13.81        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       19.23        18.74         0.26        14.47         0.03        13.25 
TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N 
       29.95        34.78        85.12        34.36        35.24        29.92 
TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       21.11        96.82        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 
       49.48        66.54        56.91        35.90        23.57        11.77 
TCGA-63-7020 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5ML TCGA-63-A5MP 
       70.13        68.15        55.30       102.67        45.57        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 
       89.29        78.28        16.37        36.16        53.88        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 
       43.10        21.07         0.99         0.92         0.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 
       25.05         0.99         2.01         1.02         2.01        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       19.00         3.02         2.01        19.00        12.03         3.98 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2800 
       24.95        25.97        40.01         4.04        22.98        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-70-6722 TCGA-77-6842 TCGA-77-6845 
        2.73         6.64        13.35        12.07        29.56        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 
       11.18       140.09         0.49        73.22        70.13         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8133 TCGA-77-8136 
       46.78        32.55        86.76        55.73        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
       17.72       104.09        11.54        26.40         6.97        66.51 
TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       54.41       132.36       150.25        22.29         5.92        61.94 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86        41.39        40.24         6.41        36.53 
TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
       34.95         1.38         1.15        29.95        18.94        19.04 
TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       24.13        30.64        34.52        10.09         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8580 TCGA-85-8582 
       22.45        16.77         5.29         3.09        36.59        38.14 
TCGA-85-8664 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
       18.08        30.97        19.86        30.48        19.73        15.85 
TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 
       14.96         3.65         2.93        22.62        10.59         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        5.26         2.30         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 
       17.69        71.01        17.46        30.81        30.67        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 
       18.15         2.01        18.58        20.71        12.89        16.11 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK 
       13.18        11.84        64.54         1.22        57.30         4.21 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52V TCGA-XC-AA0X 
       49.28        25.32         3.65        33.07        43.89         0.20 

$`3Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3416 TCGA-18-4083 TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 
       12.20        31.99         6.18        48.82        60.66        22.06 
TCGA-33-6737 TCGA-34-2605 TCGA-39-5039 TCGA-43-5668 TCGA-43-A474 TCGA-56-7221 
       19.76        28.96        17.88        18.38        11.61        19.99 
TCGA-56-8201 TCGA-60-2696 TCGA-60-2711 TCGA-94-7557 TCGA-94-A5I4 TCGA-98-A539 
       13.05         3.58        41.42         0.16        16.14         5.69 
TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3411 
       21.21        76.80        65.65        16.80        75.75       117.57 
TCGA-18-3412 TCGA-18-3415 TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 TCGA-21-1075 
       11.34        92.15       154.32        49.94        99.16        70.16 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 
       15.58        31.73       119.80         7.33        64.21         1.74 
TCGA-22-1016 TCGA-22-4594 TCGA-22-4596 TCGA-22-4604 TCGA-22-5473 TCGA-22-5474 
       27.02        48.33         0.56        13.12        63.55        14.63 
TCGA-22-5478 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5492 TCGA-33-4583 
        0.79        79.20        11.74        18.84        16.64       151.27 
TCGA-33-6738 TCGA-33-AAS8 TCGA-33-AASJ TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 
       63.35        36.62       118.36        65.23        74.66        60.30 
TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 
        4.96        38.79        26.43        33.90         0.43         0.39 
TCGA-37-4129 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5027 TCGA-39-5034 TCGA-39-5036 
        7.96        21.70       133.25       102.18        36.39        71.18 
TCGA-43-2581 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       38.66        24.89        21.47         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 TCGA-52-7622 TCGA-52-7811 
       11.77         9.73        14.20         0.39        28.34         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 
       27.45        28.96        21.90        18.48        31.27        19.76 
TCGA-56-7823 TCGA-56-8307 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-A4BX 
       33.24        26.89         1.35         1.81        22.75        13.32 
TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46L TCGA-60-2697 TCGA-60-2698 
       13.55        71.24        16.47        56.65        12.23        10.22 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 
       50.33        48.49        42.64         3.19        29.85        26.83 
TCGA-63-6202 TCGA-63-7021 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM 
       52.67        70.42        70.62        58.65        59.97        14.99 
TCGA-63-A5MN TCGA-63-A5MY TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 
       11.34        34.59         2.01         1.02         2.01        43.99 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 TCGA-66-2791 
        2.01         7.07        12.00         1.97        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7757 TCGA-68-A59I 
       30.02        10.06        54.08         4.01         6.94        16.18 
TCGA-68-A59J TCGA-70-6723 TCGA-77-6843 TCGA-77-6844 TCGA-77-7337 TCGA-77-8007 
       14.73        12.33        73.12        75.09       106.95         6.51 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 
       37.81       156.66        12.59        27.39        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-85-6175 TCGA-85-7698 TCGA-85-7699 TCGA-85-8048 
       36.36       126.18         9.67        31.30        32.91        25.15 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       31.56        26.79        32.71         2.01        15.39         7.76 
TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A50M 
       12.59        22.59        30.28        34.13        24.36        27.16 
TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 
       16.21        15.29        29.92        12.39        24.92        11.77 
TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 
       20.22         2.70         3.48        18.31        27.68        21.44 
TCGA-98-8023 TCGA-98-A53C TCGA-98-A53H TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HJ 
       21.34        27.02        20.32        13.41         4.54        13.74 
TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52Q 
        2.89        43.92        14.73        26.43        83.57         3.72 
TCGA-O2-A52S TCGA-O2-A5IB 
       12.72        11.18 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.03              0.16 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           173.82            156.66 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            21.52             21.80 
[1] "0.0 - 173.8 (21.5)" "0.2 - 156.7 (21.8)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         2       60       97        2        38        58
  3Q GAIN WILD-TYPE       0       29       55        0        27        37
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  3Q GAIN MUTATED           0         39         10        7
  3Q GAIN WILD-TYPE         3         24          9        0
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                60                29
  STAGE IB                97                55
  STAGE II                 2                 0
  STAGE IIA               38                27
  STAGE IIB               58                37
  STAGE III                0                 3
  STAGE IIIA              39                24
  STAGE IIIB              10                 9
  STAGE IV                 7                 0
[1] 10  2
[1] 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    74 189  39  13
  3Q GAIN WILD-TYPE  38 105  32  11
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              74                38
  T2             189               105
  T3              39                32
  T4              13                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
  3Q GAIN MUTATED   201  82  24   4
  3Q GAIN WILD-TYPE 116  51  16   1
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0             201               116
  N1              82                51
  N2              24                16
  N3               4                 1
[1] 4 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   255   7
  3Q GAIN WILD-TYPE 156   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    255    7
  3Q GAIN WILD-TYPE  156    0
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0             255               156
  1               7                 0
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    79 236
  3Q GAIN WILD-TYPE  51 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     79  236
  3Q GAIN WILD-TYPE   51  135
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              79                51
  MALE               236               135
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   238  35
  3Q GAIN WILD-TYPE 146  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    238   35
  3Q GAIN WILD-TYPE  146   18
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO              238               146
  YES              35                18
[1] 2 2
[1] FALSE
D6V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                      12
  3Q GAIN WILD-TYPE                                     3
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  3Q GAIN MUTATED                                        0
  3Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                         1
  3Q GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                           302
  3Q GAIN WILD-TYPE                                                         177
D6V10, multiclass
                                                             clus
vv                                                            3Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             302
                                                             clus
vv                                                            3Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               177
[1] 4 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   253   7   3  15
  3Q GAIN WILD-TYPE 146   5   1   8
D6V13, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0             253               146
  R1               7                 5
  R2               3                 1
  RX              15                 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                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       4                        22   219
  3Q GAIN WILD-TYPE     5                         9   130
D6V14, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              22                 9
  WHITE                                 219               130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5 200
  3Q GAIN WILD-TYPE   3 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5  200
  3Q GAIN WILD-TYPE    3  117
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             200               117
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    15  16
  4P GAIN WILD-TYPE 265 198
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               31               463 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               16               198 
$`4P GAIN MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-22-1017 TCGA-22-A5C4 TCGA-34-2609 TCGA-60-2715 
      123.19         4.80        48.82        22.06        31.27        35.34 
TCGA-68-8250 TCGA-96-7545 TCGA-22-4591 TCGA-22-4601 TCGA-22-5478 TCGA-34-2596 
        8.02        57.07        20.48        34.75         0.79         2.63 
TCGA-37-4130 TCGA-43-2576 TCGA-43-3920 TCGA-43-8116 TCGA-46-3769 TCGA-56-1622 
        8.12        40.21        33.11        11.77         4.44        28.96 
TCGA-63-6202 TCGA-63-A5MG TCGA-63-A5MV TCGA-66-2763 TCGA-70-6722 TCGA-77-6842 
       52.67        70.62        36.16         0.99        12.07        29.56 
TCGA-77-7337 TCGA-77-8007 TCGA-77-A5G6 TCGA-85-A4JC TCGA-90-7767 TCGA-94-A4VJ 
      106.95         6.51        22.29        19.86         2.93        14.14 
TCGA-98-8022 
       30.67 

$`4P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
       12.20         4.47        31.99         6.18        27.19        32.19 
TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 
       14.93        60.66        64.93       129.01       133.74         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 
       19.76        31.50        28.96        17.88        22.49        18.38 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
        7.76        78.18         2.93        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ 
       13.05         3.45        17.00        16.77        17.85        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH 
        0.13         3.58        41.42         9.01        32.32        66.61 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
       20.78        42.08        30.81         9.50        14.07        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
        0.16        18.38        16.14        19.36         2.76         5.69 
TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
       21.21        19.10         0.07        76.80        39.85        40.90 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       65.65        16.80         0.43         8.58        75.75       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       11.34        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2.79       154.32        49.94       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       70.16        60.89        34.78        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
        9.34       119.80        43.23        31.63        88.11        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       33.93        10.82        21.99         7.33         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
        1.74        14.10        27.02        35.08        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
        0.56        38.17        13.12        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
       11.77        63.55        14.63        44.25        86.30        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       16.64        97.94        79.53       173.82       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       14.07        54.44        63.35         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 
        6.94       110.99        44.19       118.36        27.16        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       32.88        65.23        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       50.66        16.93        44.75        39.32         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       38.79         4.04        26.43        33.90         4.01         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        0.39         7.96         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        3.39        37.58        21.70       133.25       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        60.53        36.39        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       17.06        38.66        39.12        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-A475 
       21.47         5.46         3.81        19.59        13.38         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 
       14.20        13.32        12.16        13.02         9.83        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       13.91         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
       30.35         8.75        27.45        12.43        18.25        21.90 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
       18.48        14.53        31.27        30.41        19.76         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 
        0.10        17.49        33.24        14.96         4.93         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       26.89        14.07         1.35         1.81        22.75        13.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
       10.36         9.93        20.25        15.81        20.94        19.23 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       13.32        18.74         0.26        14.47         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       13.55        29.95        71.24        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       34.36        56.65        35.24        29.92        21.11        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       10.22        96.82        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       49.48        66.54        56.91        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
        3.19        29.85        35.90        23.57        26.83        11.77 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI 
       70.13        70.42        68.15        55.30       102.67        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       59.97        45.57        14.99        11.34        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       78.28        16.37        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
        2.01        21.07         0.99         1.02         2.01         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
        0.99        43.99        21.01        25.05         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
        2.01         2.01         7.07        23.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        2.01        19.00        12.03         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1.97        25.97        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         6.94        13.35        16.18        14.73 
TCGA-70-6723 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       12.33        73.12        75.09        23.28        11.18       140.09 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        0.49        73.22        70.13         0.16        46.78        32.55 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       86.76        55.73        37.81       156.66        12.59        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       39.09        17.72       104.09        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97        66.51        54.41        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      126.18       132.36       150.25         5.92        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       38.86         9.67        41.39        40.24         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       34.95        31.30        32.91         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       18.94        25.15        19.04        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       30.64        34.52        10.09         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       16.77         5.29         3.09        32.71         2.01        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        7.76        36.59        38.14        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       30.28        34.13        30.97        24.36        30.48        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       27.16        16.21        15.85        14.96        15.29        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
       12.39         3.65        24.92        11.77        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       10.59         2.70         3.48         4.01         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        4.01         5.03        26.63        17.69        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 
       17.46        27.68        21.44        30.81        21.34        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
       18.15         2.01        27.02        20.32        18.58        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       12.89        16.11        13.18        13.41        11.84         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       64.54         1.22        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       49.28        43.92        25.32        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
        3.65        33.07         3.72        12.72        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.79              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           123.19            173.82 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            22.29             21.47 
[1] "0.8 - 123.2 (22.3)" "0.0 - 173.8 (21.5)"
[1] "hr=" "1.3"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         0        9        5        0         4         7
  4P GAIN WILD-TYPE       2       80      147        2        61        88
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  4P GAIN MUTATED           0          5          0        0
  4P GAIN WILD-TYPE         3         58         19        7
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 9                80
  STAGE IB                 5               147
  STAGE II                 0                 2
  STAGE IIA                4                61
  STAGE IIB                7                88
  STAGE III                0                 3
  STAGE IIIA               5                58
  STAGE IIIB               0                19
  STAGE IV                 0                 7
[1] 10  2
[1] 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     9  17   3   2
  4P GAIN WILD-TYPE 103 277  68  22
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               9               103
  T2              17               277
  T3               3                68
  T4               2                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                 N0  N1  N2  N3
  4P GAIN MUTATED    21   7   3   0
  4P GAIN WILD-TYPE 296 126  37   5
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              21               296
  N1               7               126
  N2               3                37
  N3               0                 5
[1] 4 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    28   0
  4P GAIN WILD-TYPE 383   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     28    0
  4P GAIN WILD-TYPE  383    7
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              28               383
  1               0                 7
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4  27
  4P GAIN WILD-TYPE 126 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4   27
  4P GAIN WILD-TYPE  126  344
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               4               126
  MALE                27               344
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    22   4
  4P GAIN WILD-TYPE 362  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     22    4
  4P GAIN WILD-TYPE  362   49
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               22               362
  YES               4                49
[1] 2 2
[1] FALSE
D7V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED                                       1
  4P GAIN WILD-TYPE                                    14
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  4P GAIN MUTATED                                        0
  4P GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED                                         0
  4P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                            30
  4P GAIN WILD-TYPE                                                         449
D7V10, multiclass
                                                             clus
vv                                                            4P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              30
                                                             clus
vv                                                            4P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               449
[1] 4 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    24   1   0   2
  4P GAIN WILD-TYPE 375  11   4  21
D7V13, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              24               375
  R1               1                11
  R2               0                 4
  RX               2                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         2    20
  4P GAIN WILD-TYPE     8                        29   329
D7V14, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               2                29
  WHITE                                  20               329
[1] 3 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     0  19
  4P GAIN WILD-TYPE   8 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   19
  4P GAIN WILD-TYPE    8  298
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              19               298
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     7  14
  4Q GAIN WILD-TYPE 273 200
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               473 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               200 
$`4Q GAIN MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-A5C4 TCGA-34-2609 TCGA-60-2715 
      123.19         4.80        31.99        22.06        31.27        35.34 
TCGA-96-7545 TCGA-22-4593 TCGA-22-4601 TCGA-22-5478 TCGA-33-6738 TCGA-34-2596 
       57.07        35.08        34.75         0.79        63.35         2.63 
TCGA-34-8456 TCGA-43-2576 TCGA-43-3920 TCGA-56-1622 TCGA-56-7579 TCGA-63-A5MV 
       26.43        40.21        33.11        28.96        31.27        36.16 
TCGA-77-7337 TCGA-85-A4JC TCGA-O2-A52N 
      106.95        19.86        33.07 

$`4Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20         4.47         6.18        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 
       48.82        60.66        64.93       129.01       133.74         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 
       19.76        31.50        28.96        17.88        22.49        18.38 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
        7.76        78.18         2.93        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ 
       13.05         3.45        17.00        16.77        17.85        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH 
        0.13         3.58        41.42         9.01        32.32        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
        8.02        20.78        42.08        30.81         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 
       21.04         0.16        18.38        16.14        19.36         2.76 
TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        5.69        21.21        19.10         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       40.90        65.65        16.80         0.43         8.58        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
      117.57        11.34        23.54        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       86.96         2.79       154.32        49.94       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       99.16        70.16        60.89        34.78        15.58        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
      122.43         9.34       119.80        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       41.69        33.93        10.82        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
       64.21         1.74        14.10        27.02        20.48        48.33 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       24.13         0.56        38.17        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
        9.57        11.77        63.55        14.63        44.25        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       71.34        79.20        11.74        18.84        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       56.32        16.64        97.94        79.53       173.82       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      151.27        14.07        54.44         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 
        6.94       110.99        44.19       118.36        27.16        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       32.88        65.23        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       50.66        16.93        44.75        39.32         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       38.79         4.04        33.90         4.01         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        7.96         8.12         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        3.39        37.58        21.70       133.25       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        60.53        36.39        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       17.06        38.66        39.12        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       21.47         5.46         3.81        19.59        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
        9.73        14.20        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        4.44        10.65        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 
       28.34         5.46        30.35         8.75        27.45        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 
       18.25        21.90        18.48        14.53        30.41        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
        6.51         0.10        17.49        33.24        14.96         4.93 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        3.48        26.89        14.07         1.35         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
       13.81        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       19.23        13.32        18.74         0.26        14.47         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.25        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       85.12        34.36        56.65        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       12.23        10.22        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       80.45        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW 
       11.34        25.28        89.29        78.28        16.37        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       34.59        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        1.02         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       25.05         0.99         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        7.07        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       12.03         3.98        12.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
       40.01        22.98         4.04        22.98         5.03        30.02 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       10.06        54.08         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 
        6.94        13.35        16.18        14.73        12.07        12.33 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       29.56        73.12        75.09        23.28        11.18       140.09 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        0.49        73.22        70.13         0.16        46.78        32.55 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        6.51        86.76        55.73        37.81       156.66        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       53.92        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       27.39         6.97        66.51        54.41        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       36.36       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       61.94        27.62        38.86         9.67        41.39        40.24 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
        6.41        36.53        34.95        31.30        32.91         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1.15        29.95        18.94        25.15        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       31.56        26.79        30.64        34.52        10.09         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       13.22        22.45        16.77         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01        15.39         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA 
       18.08        22.59        30.28        34.13        30.97        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       30.48        19.73        27.16        16.21        15.85        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 
       15.29        29.92        12.39         3.65        24.92         2.93 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       11.77        20.22        22.62        10.59         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         5.26         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       14.14        17.69        71.01        18.31        17.46        27.68 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A 
       21.44        30.81        30.67        21.34        27.16        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
        2.01        27.02        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG 
       16.11        13.18        13.41        11.84         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
        1.22        57.30        13.74         4.21         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
       43.92        25.32        14.73        26.43        83.57         3.65 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        12.72        43.89        11.18         0.20 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.79              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           123.19            173.82 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            33.07             21.07 
[1] "0.8 - 123.2 (33.1)" "0.0 - 173.8 (21.1)"
[1] "hr=" "1.3"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         1        3        3        0         5         5
  4Q GAIN WILD-TYPE       1       86      149        2        60        90
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  4Q GAIN MUTATED           0          4          0        0
  4Q GAIN WILD-TYPE         3         59         19        7
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 3                86
  STAGE IB                 3               149
  STAGE II                 0                 2
  STAGE IIA                5                60
  STAGE IIB                5                90
  STAGE III                0                 3
  STAGE IIIA               4                59
  STAGE IIIB               0                19
  STAGE IV                 0                 7
[1] 10  2
[1] 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     4  14   2   1
  4Q GAIN WILD-TYPE 108 280  69  23
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               4               108
  T2              14               280
  T3               2                69
  T4               1                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                 N0  N1  N2  N3
  4Q GAIN MUTATED    13   6   2   0
  4Q GAIN WILD-TYPE 304 127  38   5
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              13               304
  N1               6               127
  N2               2                38
  N3               0                 5
[1] 4 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    18   0
  4Q GAIN WILD-TYPE 393   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     18    0
  4Q GAIN WILD-TYPE  393    7
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              18               393
  1               0                 7
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  18
  4Q GAIN WILD-TYPE 127 353
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   18
  4Q GAIN WILD-TYPE  127  353
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               3               127
  MALE                18               353
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    17   3
  4Q GAIN WILD-TYPE 367  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     17    3
  4Q GAIN WILD-TYPE  367   50
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               17               367
  YES               3                50
[1] 2 2
[1] FALSE
D8V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED                                       1
  4Q GAIN WILD-TYPE                                    14
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  4Q GAIN MUTATED                                        0
  4Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED                                         0
  4Q GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                            20
  4Q GAIN WILD-TYPE                                                         459
D8V10, multiclass
                                                             clus
vv                                                            4Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              20
                                                             clus
vv                                                            4Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               459
[1] 4 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    17   0   0   1
  4Q GAIN WILD-TYPE 382  12   4  22
D8V13, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              17               382
  R1               0                12
  R2               0                 4
  RX               1                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         1    16
  4Q GAIN WILD-TYPE     9                        30   333
D8V14, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               1                30
  WHITE                                  16               333
[1] 3 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  13
  4Q GAIN WILD-TYPE   8 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   13
  4Q GAIN WILD-TYPE    8  304
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              13               304
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   169 135
  5P GAIN WILD-TYPE 111  79
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              304               190 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              135                79 
$`5P GAIN MUTATED`
TCGA-21-A5DI TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4533 TCGA-34-2604 TCGA-34-2609 
       32.19        60.66        22.06       133.74        31.50        31.27 
TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V 
       17.88        18.38         7.76        78.18        11.61        12.03 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
       13.05         3.45        16.77        17.85        21.04         0.13 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH TCGA-77-A5GA TCGA-90-7766 
       41.42         9.01        32.32        66.61        42.08         9.50 
TCGA-94-7557 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH 
        0.16        57.07        19.36         2.76         5.69        19.10 
TCGA-NC-A5HD TCGA-NK-A5CT TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 
        0.07        65.65         0.43         8.58       117.57        11.34 
TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 
       23.54        36.07        86.96        49.94        46.88        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 
       70.16        34.78       122.43         9.34        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
       88.11        41.69        33.93        10.82        21.99         7.33 
TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
        4.31         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4609 
       48.33        24.13         0.56        38.17        34.75         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 
       11.77        63.55        14.63        44.25         0.79        11.74 
TCGA-22-5483 TCGA-22-5492 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 
       18.84        16.64       173.82       103.53       151.27        54.44 
TCGA-33-6738 TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 
       63.35        36.62         6.94        44.19       118.36         2.63 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       61.61        32.88         9.07        60.30        50.66        16.93 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       39.32         4.96         1.12         4.04        26.43        33.90 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        4.01         0.39         7.82         6.81         0.39         3.39 
TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
       37.58       133.25       126.58        68.58        55.20        82.52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 
       24.33         1.94        60.53        68.38        71.18        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       38.66        39.12        33.11        27.91        22.98        24.89 
TCGA-43-7656 TCGA-43-8116 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       19.59        11.77        14.20        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
        4.44        10.65        13.91        29.95        28.34         5.46 
TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 TCGA-56-7222 TCGA-56-7580 TCGA-56-7582 
        8.75        28.96        21.90        18.48        30.41        19.76 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8503 
        0.10        17.49         4.93         3.48        14.07         1.35 
TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
       13.81         9.93        20.25        15.81        19.23        13.32 
TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.26         0.03        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       16.47        85.12        34.36        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
       12.23        96.82        37.94        50.33        42.64         3.19 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
       35.90        23.57        26.83        11.77        52.67        70.13 
TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP 
       68.15       102.67        58.65        45.57        11.34        25.28 
TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 
       78.28        36.16        53.88        16.96         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        0.99         1.02         0.99        43.99        21.01        25.05 
TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        1.02         7.07        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2782 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2792 
       19.00        12.00        25.97        40.01        22.98        30.02 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I 
       54.08         4.01        49.05         6.64         6.94        16.18 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 
       14.73        29.56        75.09        23.28        11.18         0.49 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       73.22       106.95         0.16        46.78        32.55         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
       86.76        55.73        37.81       156.66        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8150 
       17.72       104.09        11.54        26.40         6.97        54.41 
TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
       36.36       132.36        22.29         5.92        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 
       38.86         9.67        41.39         6.41        36.53        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 
        1.38         1.15        29.95        25.15        26.79        30.64 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8479 TCGA-85-8481 
       10.09         0.76        22.45        16.77        15.39         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       36.59        38.14        18.08        22.59        34.13        30.97 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       19.86        30.48        19.73        27.16        16.21        15.85 
TCGA-85-A511 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       14.96         2.93        11.77        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8064 TCGA-94-8035 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        3.48         5.26         4.01        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53B 
       18.31        17.46        30.81        30.67        21.34         2.01 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
       18.58        20.71        12.89        16.11        13.18        11.84 
TCGA-NC-A5HF TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HT 
        4.54        13.74         4.21        49.28        14.73        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52V TCGA-XC-AA0X 
       83.57         3.65        43.89         0.20 

$`5P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-33-4532 TCGA-33-4589 
       27.19        14.93        48.82        64.93       129.01         1.55 
TCGA-33-6737 TCGA-34-2605 TCGA-43-2578 TCGA-43-8118 TCGA-56-7221 TCGA-56-8308 
       19.76        28.96        22.49         2.93        19.99        17.00 
TCGA-60-2696 TCGA-60-2715 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB TCGA-90-7964 
        3.58        35.34         8.02        20.78        30.81        14.07 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A5I4 TCGA-98-A53D TCGA-NC-A5HE TCGA-NC-A5HM 
       21.04        18.38        16.14        21.21        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 
       40.90        16.80        75.75        92.15        92.42         2.79 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 
      154.32       119.54        60.89        15.58        31.73       119.80 
TCGA-22-1005 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5479 TCGA-22-5480 
       64.21        13.12        32.02        19.30        86.30        71.34 
TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 
       79.20        30.12        62.86        56.32        97.94        79.53 
TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASL TCGA-34-5231 
       14.07         4.70         0.30       110.99        27.16        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 
       81.24        74.66        44.75        38.79         0.43         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-A5EN TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 
        8.12         7.46        21.70       111.35       102.18         1.71 
TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       36.39        55.56        17.06        21.47         5.46         3.81 
TCGA-43-8115 TCGA-43-A475 TCGA-46-3765 TCGA-51-4079 TCGA-51-4080 TCGA-52-7810 
       13.38         9.73        13.32         0.39         0.39        30.35 
TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 
       27.45        12.43        18.25        14.53        31.27         6.51 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8307 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 
       33.24        14.96        26.89         1.81        22.75        10.36 
TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8393 TCGA-58-A46L TCGA-60-2698 
       20.94        18.74        14.47        34.78        56.65        10.22 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       92.71        21.93        80.45        49.48        66.54        56.91 
TCGA-60-2716 TCGA-60-2722 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MJ 
       48.49        29.85        70.42        55.30        70.62        59.97 
TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2734 TCGA-66-2754 
       14.99        89.29        16.37        34.59        43.10         2.01 
TCGA-66-2755 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2780 
        0.92         0.99         2.01         2.01         2.01        12.03 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
        3.98        24.95         1.97         4.04        22.98         5.03 
TCGA-66-2793 TCGA-68-7755 TCGA-68-8251 TCGA-70-6722 TCGA-70-6723 TCGA-77-6843 
       10.06         2.73        13.35        12.07        12.33        73.12 
TCGA-77-7139 TCGA-77-7335 TCGA-77-8131 TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 
      140.09        70.13        12.59        27.39        66.51        65.49 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 
       60.53       126.18       150.25        40.24        34.95        31.30 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8288 
       18.94        19.04        24.13        31.56        34.52        13.22 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8584 TCGA-85-A4CL 
        5.29         3.09        32.71         2.01        12.59        30.28 
TCGA-85-A4PA TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       24.36        15.29        29.92        12.39         3.65        24.92 
TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 TCGA-94-8490 TCGA-94-8491 TCGA-96-A4JL 
       20.22         4.01         2.30         5.03        26.63        27.68 
TCGA-98-7454 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-LA-A7SW 
       21.44        27.16        18.15        27.02        20.32        13.41 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP 
       64.54         1.22        57.30         2.89        43.92        25.32 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB 
       33.07         3.72        12.72        11.18 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           173.82            154.32 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           21.225            22.210 
[1] "0.0 - 173.8 (21.2)" "0.3 - 154.3 (22.2)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         1       53       95        2        39        62
  5P GAIN WILD-TYPE       1       36       57        0        26        33
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  5P GAIN MUTATED           0         40          9        5
  5P GAIN WILD-TYPE         3         23         10        2
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                53                36
  STAGE IB                95                57
  STAGE II                 2                 0
  STAGE IIA               39                26
  STAGE IIB               62                33
  STAGE III                0                 3
  STAGE IIIA              40                23
  STAGE IIIB               9                10
  STAGE IV                 5                 2
[1] 10  2
[1] 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    64 188  41  16
  5P GAIN WILD-TYPE  48 106  30   8
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              64                48
  T2             188               106
  T3              41                30
  T4              16                 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
  5P GAIN MUTATED   202  78  27   1
  5P GAIN WILD-TYPE 115  55  13   4
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0             202               115
  N1              78                55
  N2              27                13
  N3               1                 4
[1] 4 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   255   5
  5P GAIN WILD-TYPE 156   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    255    5
  5P GAIN WILD-TYPE  156    2
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             255               156
  1               5                 2
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    77 232
  5P GAIN WILD-TYPE  53 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     77  232
  5P GAIN WILD-TYPE   53  139
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              77                53
  MALE               232               139
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   238  31
  5P GAIN WILD-TYPE 146  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    238   31
  5P GAIN WILD-TYPE  146   22
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              238               146
  YES              31                22
[1] 2 2
[1] FALSE
D9V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                       8
  5P GAIN WILD-TYPE                                     7
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  5P GAIN MUTATED                                        2
  5P GAIN WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                         1
  5P GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                           298
  5P GAIN WILD-TYPE                                                         181
D9V10, multiclass
                                                             clus
vv                                                            5P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             298
                                                             clus
vv                                                            5P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D9V11, continuous
D9V12, continuous
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED   254   6   3   8
  5P GAIN WILD-TYPE 145   6   1  15
D9V13, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             254               145
  R1               6                 6
  R2               3                 1
  RX               8                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       3                        18   218
  5P GAIN WILD-TYPE     6                        13   131
D9V14, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              18                13
  WHITE                                 218               131
[1] 3 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     3 198
  5P GAIN WILD-TYPE   5 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  198
  5P GAIN WILD-TYPE    5  119
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO             198               119
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    50  46
  5Q GAIN WILD-TYPE 230 168
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               96               398 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               46               168 
$`5Q GAIN MUTATED`
TCGA-21-A5DI TCGA-22-A5C4 TCGA-39-5039 TCGA-43-7657 TCGA-43-7658 TCGA-43-A56V 
       32.19        22.06        17.88         7.76        78.18        12.03 
TCGA-60-2712 TCGA-63-A5MH TCGA-98-8020 TCGA-J1-A4AH TCGA-NK-A7XE TCGA-18-5592 
        9.01        66.61         2.76        19.10         0.43        49.94 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1083 TCGA-21-5782 TCGA-22-1012 TCGA-22-1016 
       46.88        70.16        43.23        31.63        14.10        27.02 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4613 TCGA-22-5478 TCGA-22-5482 TCGA-22-5483 
       24.13         0.56        11.77         0.79        11.74        18.84 
TCGA-33-4582 TCGA-33-4583 TCGA-34-2596 TCGA-34-5236 TCGA-34-5241 TCGA-34-5928 
      103.53       151.27         2.63         9.07        16.93        39.32 
TCGA-34-A5IX TCGA-37-3792 TCGA-37-5819 TCGA-39-5021 TCGA-39-5029 TCGA-39-5031 
       33.90         0.39         3.39        68.58        24.33        60.53 
TCGA-43-3920 TCGA-43-6143 TCGA-46-3767 TCGA-56-1622 TCGA-56-7222 TCGA-56-7580 
       33.11        22.98        13.02        28.96        18.48        30.41 
TCGA-56-8083 TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 TCGA-58-8386 TCGA-58-A46M 
        4.93         1.35        13.81         9.93         0.03        35.24 
TCGA-58-A46N TCGA-60-2703 TCGA-60-2719 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MI 
       29.92        96.82        42.64        23.57        26.83        58.65 
TCGA-63-A5MN TCGA-63-A5MV TCGA-66-2744 TCGA-66-2758 TCGA-66-2771 TCGA-66-2778 
       11.34        36.16         0.99        21.01        19.00        19.00 
TCGA-66-2786 TCGA-66-2792 TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7337 
       25.97        30.02        29.56        75.09        11.18       106.95 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8130 TCGA-77-8133 TCGA-77-8150 
       46.78        32.55        86.76       156.66        53.92        54.41 
TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-6175 TCGA-85-7699 
       36.36        22.29         5.92        27.62         9.67        32.91 
TCGA-85-8048 TCGA-85-8350 TCGA-85-8582 TCGA-85-A4QQ TCGA-85-A510 TCGA-90-7769 
       25.15        22.45        38.14        30.48        15.85        11.77 
TCGA-90-A59Q TCGA-92-7340 TCGA-96-8169 TCGA-96-8170 TCGA-98-A53I TCGA-98-A53J 
       10.59         2.70        18.31        17.46        18.58        20.71 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HN TCGA-NC-A5HT TCGA-NK-A5CR TCGA-XC-AA0X 
       13.18        11.84        49.28        26.43        83.57         0.20 

$`5Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 
       27.19        14.93        48.82        60.66        64.93       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      133.74         1.55        19.76        31.50        28.96        31.27 
TCGA-43-2578 TCGA-43-5668 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 
       22.49        18.38         2.93        11.61        19.99        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
        3.45        17.00        16.77        17.85        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 
        3.58        41.42        35.34        32.32         8.02        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       42.08        30.81         9.50        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D 
       18.38        16.14        57.07        19.36         5.69        21.21 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
        0.07        76.80        39.85        40.90        65.65        16.80 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
        8.58        75.75       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 
       36.07        92.42        86.96         2.79       154.32       119.54 
TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       99.16        60.89        34.78        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        9.34       119.80        88.11        41.69        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-4591 
       21.99         7.33         4.31        64.21         1.74        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       35.08        48.33        38.17        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
       19.30         9.57        63.55        14.63        44.25        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       71.34        79.20        30.12        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
       97.94        79.53       173.82        14.07        54.44        63.35 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
        4.70         0.30        36.62         6.94       110.99        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
      118.36        27.16        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
       74.66        60.30        50.66        44.75         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
       38.79         4.04        26.43         4.01         0.43         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL 
        8.12         7.46         7.82         6.81         0.39        37.58 
TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 
       21.70       133.25       126.58       111.35        55.20        82.52 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
      102.18         1.71         1.94        36.39        68.38        71.18 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 
       55.56        17.06        40.21        38.66        39.12        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3768 
       11.77         9.73        14.20        13.32        12.16         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        4.44        10.65        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 
       28.34         5.46        30.35         8.75        27.45        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
       18.25        21.90        14.53        31.27        19.76         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 
        0.10        17.49        33.24        14.96         3.48        26.89 
TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
       14.07         1.81        22.75        10.36        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       20.94        19.23        13.32        18.74         0.26        14.47 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.25        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 
       85.12        34.36        56.65        21.11        12.23        10.22 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       56.91        50.33        48.49         3.19        29.85        35.90 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MP 
      102.67        70.62        59.97        45.57        14.99        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       89.29        78.28        16.37        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       43.10         2.01        21.07         1.02         2.01         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
        0.99        43.99        25.05         0.99         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
        2.01         2.01         7.07        23.01         3.02         2.01 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
       12.03         3.98        12.00        24.95         1.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 
       22.98         4.04        22.98         5.03        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
        4.01        49.05         2.73         6.64         6.94        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6843 TCGA-77-6845 
       16.18        14.73        12.07        12.33        73.12        23.28 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-8007 
      140.09         0.49        73.22        70.13         0.16         6.51 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       55.73        37.81        12.59        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
       11.54        26.40        27.39         6.97        66.51        65.49 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GH 
       60.53       126.18       132.36       150.25        61.94        38.86 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       41.39        40.24         6.41        36.53        34.95        31.30 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
        1.38         1.15        29.95        18.94        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       31.56        26.79        30.64        34.52        10.09         0.76 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       13.22        16.77         5.29         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
       15.39         7.76        36.59        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR 
       30.28        34.13        30.97        19.86        24.36        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       27.16        16.21        14.96        15.29        29.92        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 
        3.65        24.92         2.93        20.22        22.62         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         5.26         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       14.14        17.69        71.01        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.67        21.34        27.16        18.15         2.01        27.02 
TCGA-98-A53H TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG 
       20.32        12.89        16.11        13.41         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO 
        1.22        57.30        13.74         4.21         2.89        43.92 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       25.32        14.73         3.65        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB 
       43.89        11.18 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           156.66            173.82 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           23.275            21.275 
[1] "0.0 - 156.7 (23.3)" "0.1 - 173.8 (21.3)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         0       19       28        0        13        22
  5Q GAIN WILD-TYPE       2       70      124        2        52        73
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  5Q GAIN MUTATED           0         12          2        1
  5Q GAIN WILD-TYPE         3         51         17        6
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                19                70
  STAGE IB                28               124
  STAGE II                 0                 2
  STAGE IIA               13                52
  STAGE IIB               22                73
  STAGE III                0                 3
  STAGE IIIA              12                51
  STAGE IIIB               2                17
  STAGE IV                 1                 6
[1] 10  2
[1] 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    25  57  13   2
  5Q GAIN WILD-TYPE  87 237  58  22
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              25                87
  T2              57               237
  T3              13                58
  T4               2                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                 N0  N1  N2  N3
  5Q GAIN MUTATED    59  28   8   1
  5Q GAIN WILD-TYPE 258 105  32   4
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              59               258
  N1              28               105
  N2               8                32
  N3               1                 4
[1] 4 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   1
  5Q GAIN WILD-TYPE 327   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     84    1
  5Q GAIN WILD-TYPE  327    6
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              84               327
  1               1                 6
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    22  75
  5Q GAIN WILD-TYPE 108 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     22   75
  5Q GAIN WILD-TYPE  108  296
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              22               108
  MALE                75               296
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    82   7
  5Q GAIN WILD-TYPE 302  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     82    7
  5Q GAIN WILD-TYPE  302   46
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               82               302
  YES               7                46
[1] 2 2
[1] FALSE
D10V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED                                       2
  5Q GAIN WILD-TYPE                                    13
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  5Q GAIN MUTATED                                        0
  5Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED                                         0
  5Q GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                            95
  5Q GAIN WILD-TYPE                                                         384
D10V10, multiclass
                                                             clus
vv                                                            5Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              95
                                                             clus
vv                                                            5Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               384
[1] 4 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    80   2   1   1
  5Q GAIN WILD-TYPE 319  10   3  22
D10V13, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              80               319
  R1               2                10
  R2               1                 3
  RX               1                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         4    68
  5Q GAIN WILD-TYPE     9                        27   281
D10V14, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               4                27
  WHITE                                  68               281
[1] 3 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  57
  5Q GAIN WILD-TYPE   7 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   57
  5Q GAIN WILD-TYPE    7  260
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              57               260
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    62  44
  6P GAIN WILD-TYPE 218 170
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              106               388 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               44               170 
$`6P GAIN MUTATED`
TCGA-18-3409 TCGA-33-4533 TCGA-33-4589 TCGA-34-2609 TCGA-43-2578 TCGA-56-8308 
      123.19       133.74         1.55        31.27        22.49        17.00 
TCGA-60-2715 TCGA-63-A5MH TCGA-94-7943 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
       35.34        66.61        18.38         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-O2-A52W TCGA-21-1072 TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 
       40.90         8.58        99.16        34.78        31.73       119.80 
TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-4601 TCGA-22-4605 
       43.23        33.93        10.82         4.31        34.75        32.02 
TCGA-22-4607 TCGA-22-5482 TCGA-33-4582 TCGA-33-4587 TCGA-33-AAS8 TCGA-33-AASI 
       19.30        11.74       103.53        54.44        36.62        44.19 
TCGA-34-5928 TCGA-34-7107 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 
       39.32         1.12         8.12         7.46         7.82         0.39 
TCGA-37-A5EL TCGA-39-5019 TCGA-39-5022 TCGA-43-3394 TCGA-43-5670 TCGA-43-6770 
       37.58       111.35        55.20        39.12        27.91        21.47 
TCGA-46-3769 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 
        4.44        13.91         5.46        30.35        28.96        18.25 
TCGA-56-6545 TCGA-56-7730 TCGA-56-8629 TCGA-56-A49D TCGA-58-8387 TCGA-58-8393 
       21.90         6.51        15.81        20.94        13.25        34.78 
TCGA-58-A46K TCGA-60-2703 TCGA-60-2714 TCGA-60-2719 TCGA-60-2725 TCGA-63-6202 
       34.36        96.82        50.33        42.64        26.83        52.67 
TCGA-63-A5MI TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2734 TCGA-66-2754 
       58.65        78.28        16.37        53.88        43.10         2.01 
TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 TCGA-66-2777 TCGA-66-2781 
       43.99         2.01         1.02         7.07         2.01         3.98 
TCGA-66-2791 TCGA-66-2793 TCGA-68-8251 TCGA-77-7141 TCGA-77-7142 TCGA-77-7465 
        5.03        10.06        13.35         0.49        73.22        32.55 
TCGA-77-8130 TCGA-77-8156 TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7699 
      156.66        36.36         9.67        41.39         6.41        32.91 
TCGA-85-7843 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8353 
        1.15        24.13        30.64        34.52         0.76         3.09 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4QR TCGA-90-A4EE TCGA-90-A59Q 
       38.14        12.59        30.97        19.73        22.62        10.59 
TCGA-98-7454 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B TCGA-LA-A446 TCGA-LA-A7SW 
       21.44        30.67        27.16         2.01        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HK TCGA-NC-A5HT 
       11.84        64.54         4.21        26.43 

$`6P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-5668 
      129.01        19.76        31.50        28.96        17.88        18.38 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
        7.76        78.18         2.93        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
       13.05         3.45        16.77        17.85        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 
        3.58        41.42         9.01        32.32         8.02        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       42.08        30.81         9.50        14.07        21.04         0.16 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D 
       16.14        57.07        19.36         2.76         5.69        21.21 
TCGA-J1-A4AH TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3411 
       19.10        65.65        16.80         0.43        75.75       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       11.34        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
        2.79       154.32        49.94       119.54        46.88        70.16 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 
       60.89        15.58       122.43         9.34        31.63        88.11 
TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       41.69        21.99         7.33        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       27.02        20.48        35.08        48.33        24.13         0.56 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       38.17        13.12         9.57        11.77        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 
       44.25         0.79        86.30        71.34        79.20        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 
       30.12        62.86        56.32        16.64        97.94        79.53 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
      173.82       151.27        14.07        63.35         4.70         0.30 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
        6.94       110.99       118.36        27.16         2.63        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       32.88        65.23        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 
       50.66        16.93        44.75         4.96        38.79         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       26.43        33.90         4.01         0.43         0.39         7.96 
TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 
        6.81         3.39        21.70       133.25       126.58        68.58 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       36.39        68.38        71.18        55.56        17.06        40.21 
TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 
       38.66        33.11        22.98        24.89         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
       19.59        13.38        11.77         9.73        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
       12.16        13.02         9.83        10.65         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-7222 
       29.95        28.34         8.75        27.45        12.43        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
       14.53        31.27        30.41        19.76         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       33.24        14.96         4.93         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       20.25        19.23        13.32        18.74         0.26        14.47 
TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J 
        0.03        13.55        29.95        71.24        16.47        85.12 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 
       56.65        35.24        29.92        21.11        12.23        10.22 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       56.91        48.49         3.19        29.85        35.90        23.57 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       11.77        70.13        70.42        68.15        55.30       102.67 
TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       70.62        59.97        45.57        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 
       89.29        36.16        34.59        16.96         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 
        0.99         1.02         0.92         0.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
        0.99         2.01         2.01        23.01        19.00         3.02 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       19.00        12.03        12.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 
       40.01        22.98         4.04        22.98        30.02        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I 
        4.01        49.05         2.73         6.64         6.94        16.18 
TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       14.73        12.07        12.33        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       23.28        11.18       140.09        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 
       46.78         6.51        86.76        55.73        37.81        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       53.92        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       27.39         6.97        66.51        54.41        65.49        60.53 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       150.25        22.29         5.92        61.94 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       27.62        38.86        40.24        36.53        34.95        31.30 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 
        1.38        29.95        18.94        25.15        19.04        31.56 
TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       26.79        10.09        13.22        22.45        16.77         5.29 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 
       32.71         2.01        15.39         7.76        36.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       22.59        30.28        34.13        19.86        24.36        30.48 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       27.16        16.21        15.85        14.96        15.29        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
       12.39         3.65        24.92         2.93        11.77        20.22 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
        2.70         3.48         4.01         5.26         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        5.03        26.63        14.14        17.69        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53C 
       17.46        27.68        30.81        21.34        18.15        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HF 
       20.32        18.58        20.71        12.89        16.11         4.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO 
        1.22        57.30        13.74         2.89        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q 
       25.32        14.73        83.57         3.65        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89        11.18         0.20 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.07              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           156.66            173.82 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           26.630            21.055 
[1] "0.1 - 156.7 (26.6)" "0.0 - 173.8 (21.1)"
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         1       18       34        1        14        20
  6P GAIN WILD-TYPE       1       71      118        1        51        75
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  6P GAIN MUTATED           0         15          3        1
  6P GAIN WILD-TYPE         3         48         16        6
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                18                71
  STAGE IB                34               118
  STAGE II                 1                 1
  STAGE IIA               14                51
  STAGE IIB               20                75
  STAGE III                0                 3
  STAGE IIIA              15                48
  STAGE IIIB               3                16
  STAGE IV                 1                 6
[1] 10  2
[1] 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    21  66  15   6
  6P GAIN WILD-TYPE  91 228  56  18
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              21                91
  T2              66               228
  T3              15                56
  T4               6                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
  6P GAIN MUTATED    76  23   7   1
  6P GAIN WILD-TYPE 241 110  33   4
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              76               241
  N1              23               110
  N2               7                33
  N3               1                 4
[1] 4 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    91   1
  6P GAIN WILD-TYPE 320   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     91    1
  6P GAIN WILD-TYPE  320    6
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              91               320
  1               1                 6
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    25  83
  6P GAIN WILD-TYPE 105 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     25   83
  6P GAIN WILD-TYPE  105  288
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              25               105
  MALE                83               288
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    74  17
  6P GAIN WILD-TYPE 310  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     74   17
  6P GAIN WILD-TYPE  310   36
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               74               310
  YES              17                36
[1] 2 2
[1] FALSE
D11V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                       5
  6P GAIN WILD-TYPE                                    10
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  6P GAIN MUTATED                                        1
  6P GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                         1
  6P GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                           101
  6P GAIN WILD-TYPE                                                         378
D11V10, multiclass
                                                             clus
vv                                                            6P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             101
                                                             clus
vv                                                            6P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               378
[1] 4 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    87   5   1   4
  6P GAIN WILD-TYPE 312   7   3  19
D11V13, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              87               312
  R1               5                 7
  R2               1                 3
  RX               4                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       0                        10    79
  6P GAIN WILD-TYPE     9                        21   270
D11V14, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN              10                21
  WHITE                                  79               270
[1] 3 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     2  71
  6P GAIN WILD-TYPE   6 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2   71
  6P GAIN WILD-TYPE    6  246
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              71               246
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    53  38
  6Q GAIN WILD-TYPE 227 176
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               91               403 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               38               176 
$`6Q GAIN MUTATED`
TCGA-33-4533 TCGA-33-4589 TCGA-43-2578 TCGA-56-8308 TCGA-56-A5DR TCGA-60-2715 
      133.74         1.55        22.49        17.00         0.13        35.34 
TCGA-63-A5MH TCGA-94-7943 TCGA-94-A5I4 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
       66.61        18.38        16.14         0.07        76.80        39.85 
TCGA-O2-A52W TCGA-21-1072 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-22-4605 
        8.58        99.16       119.80        43.23        33.93        32.02 
TCGA-22-5477 TCGA-22-5482 TCGA-22-5483 TCGA-33-4547 TCGA-33-4587 TCGA-33-AAS8 
       44.25        11.74        18.84        79.53        54.44        36.62 
TCGA-34-7107 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-39-5019 
        1.12         7.82         6.81         0.39        37.58       111.35 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 TCGA-46-3768 TCGA-46-3769 TCGA-46-6026 
       33.11        27.91        21.47         9.83         4.44        13.91 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 TCGA-56-7822 
        5.46        30.35         8.75        28.96        21.90        17.49 
TCGA-56-8082 TCGA-56-A49D TCGA-58-8387 TCGA-58-8393 TCGA-58-A46K TCGA-60-2703 
       14.96        20.94        13.25        34.78        34.36        96.82 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2725 TCGA-63-6202 TCGA-63-A5MS TCGA-63-A5MT 
       50.33        42.64        26.83        52.67        78.28        16.37 
TCGA-66-2734 TCGA-66-2757 TCGA-66-2765 TCGA-66-2769 TCGA-66-2777 TCGA-66-2781 
       43.10        43.99         2.01         7.07         2.01         3.98 
TCGA-66-2786 TCGA-66-2789 TCGA-66-2793 TCGA-68-8251 TCGA-77-7142 TCGA-77-7465 
       25.97         4.04        10.06        13.35        73.22        32.55 
TCGA-77-8130 TCGA-85-6798 TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 TCGA-85-8276 
      156.66         6.41        32.91         1.15        18.94        34.52 
TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
        0.76         5.29         3.09        22.59        34.13        30.97 
TCGA-90-A4EE TCGA-90-A59Q TCGA-94-A4VJ TCGA-98-7454 TCGA-98-8022 TCGA-98-A53B 
       22.62        10.59        14.14        21.44        30.67         2.01 
TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HT TCGA-NK-A5CR 
       20.71        13.18        13.41        11.84        26.43        83.57 
TCGA-O2-A5IB 
       11.18 

$`6Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 
       27.19        32.19        14.93        48.82        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
       22.06       129.01        19.76        31.50        28.96        31.27 
TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
       17.88        18.38         7.76        78.18         2.93        11.61 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY 
       12.03        19.99        13.05         3.45        16.77        17.85 
TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-68-8250 
       21.04         3.58        41.42         9.01        32.32         8.02 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
       20.78        42.08        30.81         9.50        14.07        21.04 
TCGA-94-7557 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D 
        0.16        57.07        19.36         2.76         5.69        21.21 
TCGA-J1-A4AH TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 
       19.10        40.90        65.65        16.80         0.43        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
      117.57        11.34        23.54        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       86.96         2.79       154.32        49.94       119.54        46.88 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       70.16        60.89        34.78        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 
        9.34        31.63        88.11        41.69        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        7.33         4.31        64.21         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       20.48        35.08        48.33        24.13         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       34.75        13.12        19.30         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 
       14.63         0.79        86.30        71.34        79.20        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 
       62.86        56.32        16.64        97.94       173.82       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB 
      151.27        14.07        63.35         4.70         0.30         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
      110.99        44.19       118.36        27.16         2.63        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       32.88        65.23        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 
       50.66        16.93        44.75        39.32         4.96        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
        4.04        26.43        33.90         4.01         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 
        7.96         8.12         7.46         3.39        21.70       133.25 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      126.58        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        60.53        36.39        68.38        71.18 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-6143 
       55.56        17.06        40.21        38.66        39.12        22.98 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       24.89         5.46         3.81        19.59        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-6025 
        9.73        14.20        13.32        12.16        13.02        10.65 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 
        0.39         0.39        29.95        28.34        27.45        12.43 
TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
       18.25        18.48        14.53        31.27        30.41        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
        6.51         0.10        33.24         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK 
        9.93        20.25        15.81        19.23        13.32        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.26        14.47         0.03        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       16.47        85.12        56.65        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       12.23        10.22        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 
       49.48        66.54        56.91        48.49         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       35.90        23.57        11.77        70.13        70.42        68.15 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
       55.30       102.67        70.62        58.65        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MV TCGA-63-A5MW 
       14.99        11.34        25.28        89.29        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       34.59        16.96         2.01        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        2.01         0.92         0.99        21.01        25.05         0.99 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
        1.02         2.01         2.01        23.01        19.00         3.02 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
       19.00        12.03        12.00        24.95         1.97        40.01 
TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
       22.98        22.98         5.03        30.02        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J 
       49.05         2.73         6.64         6.94        16.18        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       11.18       140.09         0.49        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 
       46.78         6.51        86.76        55.73        37.81        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       53.92        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       27.39         6.97        66.51        54.41        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       36.36       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       61.94        27.62        38.86         9.67        41.39        40.24 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 
       36.53        34.95        31.30         1.38        29.95        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 
       19.04        24.13        31.56        26.79        30.64        10.09 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       13.22        22.45        16.77        32.71         2.01        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL 
        7.76        36.59        38.14        12.59        18.08        30.28 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       19.86        24.36        30.48        19.73        27.16        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       15.85        14.96        15.29        29.92        12.39         3.65 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 
       24.92         2.93        11.77        20.22         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         5.26         2.30         4.01         5.03        26.63 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 
       17.69        71.01        18.31        17.46        27.68        30.81 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       21.34        27.16        18.15        27.02        20.32        18.58 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       12.89        16.11         4.54        64.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21         2.89        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       14.73         3.65        33.07         3.72        12.72        43.89 
TCGA-XC-AA0X 
        0.20 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.07              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           156.66            173.82 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            21.47             21.93 
[1] "0.1 - 156.7 (21.5)" "0.0 - 173.8 (21.9)"
[1] "hr=" "1"  
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         1       15       34        1        12        14
  6Q GAIN WILD-TYPE       1       74      118        1        53        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  6Q GAIN MUTATED           1         10          3        0
  6Q GAIN WILD-TYPE         2         53         16        7
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                15                74
  STAGE IB                34               118
  STAGE II                 1                 1
  STAGE IIA               12                53
  STAGE IIB               14                81
  STAGE III                1                 2
  STAGE IIIA              10                53
  STAGE IIIB               3                16
  STAGE IV                 0                 7
[1] 10  2
[1] 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  55  13   5
  6Q GAIN WILD-TYPE  93 239  58  19
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              19                93
  T2              55               239
  T3              13                58
  T4               5                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
  6Q GAIN MUTATED    65  23   2   1
  6Q GAIN WILD-TYPE 252 110  38   4
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              65               252
  N1              23               110
  N2               2                38
  N3               1                 4
[1] 4 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    74   0
  6Q GAIN WILD-TYPE 337   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     74    0
  6Q GAIN WILD-TYPE  337    7
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              74               337
  1               0                 7
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    22  70
  6Q GAIN WILD-TYPE 108 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     22   70
  6Q GAIN WILD-TYPE  108  301
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              22               108
  MALE                70               301
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    64  14
  6Q GAIN WILD-TYPE 320  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     64   14
  6Q GAIN WILD-TYPE  320   39
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               64               320
  YES              14                39
[1] 2 2
[1] FALSE
D12V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED                                       2
  6Q GAIN WILD-TYPE                                    13
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  6Q GAIN MUTATED                                        0
  6Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED                                         1
  6Q GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                            89
  6Q GAIN WILD-TYPE                                                         390
D12V10, multiclass
                                                             clus
vv                                                            6Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              89
                                                             clus
vv                                                            6Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               390
[1] 4 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    71   3   1   4
  6Q GAIN WILD-TYPE 328   9   3  19
D12V13, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              71               328
  R1               3                 9
  R2               1                 3
  RX               4                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         6    70
  6Q GAIN WILD-TYPE     9                        25   279
D12V14, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               6                25
  WHITE                                  70               279
[1] 3 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     3  62
  6Q GAIN WILD-TYPE   5 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   62
  6Q GAIN WILD-TYPE    5  255
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              62               255
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   138  96
  7P GAIN WILD-TYPE 142 118
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              234               260 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               96               118 
$`7P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-4083 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 
        4.47       123.19         6.18        48.82        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-34-2605 TCGA-34-2609 TCGA-43-5668 
       22.06       133.74         1.55        28.96        31.27        18.38 
TCGA-43-7657 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8504 
        7.76        11.61        12.03        19.99        13.05        16.77 
TCGA-56-A5DR TCGA-60-2711 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
        0.13        41.42        66.61         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-94-7557 TCGA-96-7545 TCGA-96-A4JK TCGA-NC-A5HE TCGA-NC-A5HM 
       30.81         0.16        57.07        19.36        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 
       40.90         0.43         8.58        75.75       117.57        11.34 
TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       23.54        36.07        86.96       154.32        49.94       119.54 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1081 TCGA-21-5783 
       99.16        70.16        60.89        31.73         9.34        88.11 
TCGA-21-5784 TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
       41.69         7.33         1.74        14.10        20.48        35.08 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-5473 
       24.13         0.56        38.17        13.12        32.02        63.55 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 
       44.25         0.79        86.30        11.74        18.84        56.32 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-A4WN TCGA-33-AASD 
       97.94       173.82       103.53        14.07         4.70       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-5231 TCGA-34-5234 TCGA-34-5236 
       44.19        27.16         2.63        65.23        74.66         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
       50.66        16.93        39.32        26.43        33.90         4.01 
TCGA-37-3792 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN 
        0.39         8.12         6.81         0.39        37.58        21.70 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 
      133.25       126.58       111.35        60.53        68.38        55.56 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
       40.21        38.66        39.12        33.11        27.91        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-A475 TCGA-46-3765 TCGA-46-3768 TCGA-46-3769 
        5.46         3.81         9.73        13.32         9.83         4.44 
TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-56-7223 TCGA-56-7579 
       10.65         0.39        29.95         5.46        14.53        31.27 
TCGA-56-7582 TCGA-56-8304 TCGA-56-8624 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BX 
       19.76         3.48        13.81         9.93        20.94        13.32 
TCGA-56-A62T TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N 
       14.47        71.24        16.47        34.78        35.24        29.92 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2713 TCGA-60-2714 
       37.94        92.71        80.45        49.48        56.91        50.33 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
       42.64        29.85        35.90        11.77        52.67        70.13 
TCGA-63-7021 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR 
       70.42       102.67        58.65        59.97        45.57        89.29 
TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       16.37        53.88        43.10         2.01        21.07         0.99 
TCGA-66-2755 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 
        0.92        25.05         0.99         1.02         2.01        23.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 
       19.00         2.01        12.03        12.00         1.97        40.01 
TCGA-66-2791 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-70-6722 
        5.03         4.01        49.05         2.73        14.73        12.07 
TCGA-70-6723 TCGA-77-6845 TCGA-77-7138 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       12.33        23.28        11.18         0.16        46.78        32.55 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 
        6.51        86.76        55.73        37.81       156.66        53.92 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G3 
       39.09       104.09        66.51        54.41        36.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 
       22.29         5.92        61.94        27.62         9.67        40.24 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
        6.41        36.53        34.95         1.15        29.95        18.94 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8352 TCGA-85-8354 
       19.04        24.13        30.64        34.52         5.29        32.71 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       18.08        22.59        34.13        30.48        19.73        27.16 
TCGA-85-A513 TCGA-85-A53L TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       29.92        12.39        11.77        20.22        22.62        10.59 
TCGA-92-7341 TCGA-92-8064 TCGA-94-A5I6 TCGA-96-A4JL TCGA-98-8023 TCGA-98-A53I 
        3.48         5.26        17.69        27.68        21.34        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HG 
       20.71        12.89        16.11        13.41        11.84        64.54 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q 
       57.30         2.89        25.32        83.57        33.07         3.72 

$`7P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20         4.80        31.99        27.19        32.19        14.93 
TCGA-33-4532 TCGA-33-6737 TCGA-34-2604 TCGA-39-5039 TCGA-43-2578 TCGA-43-7658 
      129.01        19.76        31.50        17.88        22.49        78.18 
TCGA-43-8118 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 
        2.93         3.45        17.00        17.85        21.04         3.58 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
        9.01        35.34        32.32         9.50        14.07        21.04 
TCGA-94-7943 TCGA-94-A5I4 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH 
       18.38        16.14         2.76         5.69        21.21        19.10 
TCGA-NC-A5HD TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 
        0.07        65.65        16.80        92.15        92.42         2.79 
TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
       46.88        34.78        15.58       122.43       119.80        43.23 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 
       31.63        33.93        10.82        21.99         4.31        64.21 
TCGA-22-1016 TCGA-22-4594 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       27.02        48.33        34.75        19.30         9.57        11.77 
TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 
       14.63        71.34        79.20        30.12        62.86        16.64 
TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AAS8 
       79.53       151.27        54.44        63.35         0.30        36.62 
TCGA-33-AASB TCGA-33-AASJ TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5239 
        6.94       118.36        61.61        32.88        81.24        60.30 
TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-37-3789 
       44.75         4.96         1.12        38.79         4.04         0.43 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 
        7.96         7.46         7.82         3.39        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
       82.52       102.18         1.71        24.33         1.94        36.39 
TCGA-39-5036 TCGA-39-5040 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-8115 
       71.18        17.06        22.98        21.47        19.59        13.38 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-6026 TCGA-51-4080 
       11.77        14.20        12.16        13.02        13.91         0.39 
TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
       28.34        30.35         8.75        27.45        28.96        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
       18.25        21.90        18.48        30.41         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 
       17.49        33.24        14.96         4.93        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
        1.35         1.81        22.75        10.36        20.25        15.81 
TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       19.23        18.74         0.26         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2695 TCGA-60-2697 
       29.95        85.12        34.36        56.65        21.11        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 TCGA-60-2710 TCGA-60-2716 TCGA-60-2720 
       10.22        96.82        21.93        66.54        48.49         3.19 
TCGA-60-2724 TCGA-60-2725 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MM 
       23.57        26.83        68.15        55.30        70.62        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 
       11.34        25.28        78.28        36.16        34.59        16.96 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2765 
        1.02         2.01         0.99        43.99        21.01         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 
        2.01         7.07         3.02        19.00         3.98        24.95 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 
       25.97        22.98         4.04        22.98        30.02        10.06 
TCGA-66-2794 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
       54.08         6.64         6.94        13.35        16.18        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       73.12        75.09       140.09         0.49        73.22        70.13 
TCGA-77-7337 TCGA-77-8131 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
      106.95        12.59        17.72        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GH 
        6.97        65.49        60.53       126.18       132.36        38.86 
TCGA-85-6560 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-8048 TCGA-85-8070 
       41.39        31.30        32.91         1.38        25.15        31.56 
TCGA-85-8071 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       26.79        10.09         0.76        13.22        22.45        16.77 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        3.09         2.01        15.39         7.76        36.59        38.14 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50Z 
       12.59        30.28        30.97        19.86        24.36        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 
       15.85        14.96        15.29         3.65        24.92         2.93 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        2.70         4.01         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 
       14.14        71.01        18.31        17.46        21.44        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       30.67        27.16        18.15         2.01        27.02        20.32 
TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN 
       13.18         4.54         1.22        13.74         4.21        49.28 
TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V 
       43.92        14.73        26.43         3.65        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.13              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           173.82            151.27 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           25.875            19.445 
[1] "0.1 - 173.8 (25.9)" "0.0 - 151.3 (19.4)"
[1] "hr=" "1.4"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         2       31       80        0        30        51
  7P GAIN WILD-TYPE       0       58       72        2        35        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  7P GAIN MUTATED           1         29          7        4
  7P GAIN WILD-TYPE         2         34         12        3
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                31                58
  STAGE IB                80                72
  STAGE II                 0                 2
  STAGE IIA               30                35
  STAGE IIB               51                44
  STAGE III                1                 2
  STAGE IIIA              29                34
  STAGE IIIB               7                12
  STAGE IV                 4                 3
[1] 10  2
[1] 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    39 156  36   7
  7P GAIN WILD-TYPE  73 138  35  17
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              39                73
  T2             156               138
  T3              36                35
  T4               7                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
  7P GAIN MUTATED   145  70  18   2
  7P GAIN WILD-TYPE 172  63  22   3
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             145               172
  N1              70                63
  N2              18                22
  N3               2                 3
[1] 4 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   197   4
  7P GAIN WILD-TYPE 214   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    197    4
  7P GAIN WILD-TYPE  214    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             197               214
  1               4                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    54 184
  7P GAIN WILD-TYPE  76 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     54  184
  7P GAIN WILD-TYPE   76  187
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              54                76
  MALE               184               187
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   182  26
  7P GAIN WILD-TYPE 202  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    182   26
  7P GAIN WILD-TYPE  202   27
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              182               202
  YES              26                27
[1] 2 2
[1] FALSE
D13V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED                                       7
  7P GAIN WILD-TYPE                                     8
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  7P GAIN MUTATED                                        1
  7P GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED                                         0
  7P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                           230
  7P GAIN WILD-TYPE                                                         249
D13V10, multiclass
                                                             clus
vv                                                            7P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             230
                                                             clus
vv                                                            7P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D13V11, continuous
D13V12, continuous
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   193   5   1  11
  7P GAIN WILD-TYPE 206   7   3  12
D13V13, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             193               206
  R1               5                 7
  R2               1                 3
  RX              11                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       8                        17   154
  7P GAIN WILD-TYPE     1                        14   195
D13V14, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   8                 1
  BLACK OR AFRICAN AMERICAN              17                14
  WHITE                                 154               195
[1] 3 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     2 147
  7P GAIN WILD-TYPE   6 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2  147
  7P GAIN WILD-TYPE    6  170
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO             147               170
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   129  88
  7Q GAIN WILD-TYPE 151 126
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              217               277 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               88               126 
$`7Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1017 TCGA-22-5471 
        4.47       123.19         6.18        32.19        48.82        60.66 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-34-2605 TCGA-34-2609 
       64.93        22.06       133.74         1.55        28.96        31.27 
TCGA-43-5668 TCGA-43-7657 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8308 
       18.38         7.76        11.61        12.03        19.99        17.00 
TCGA-56-8504 TCGA-56-A5DR TCGA-60-2711 TCGA-68-8250 TCGA-77-A5GA TCGA-96-7545 
       16.77         0.13        41.42         8.02        42.08        57.07 
TCGA-96-A4JK TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       19.36        76.80        40.90         0.43         8.58        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-4721 TCGA-21-1070 
      117.57        11.34        23.54        36.07       154.32       119.54 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1081 TCGA-21-5783 
       70.16        60.89        34.78        31.73         9.34        88.11 
TCGA-21-5787 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
       10.82         1.74        14.10        20.48        35.08        48.33 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-5473 
       24.13         0.56        38.17        13.12        32.02        63.55 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5483 TCGA-22-5491 TCGA-22-5492 
       44.25         0.79        86.30        18.84        56.32        16.64 
TCGA-33-4538 TCGA-33-4586 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL 
       97.94        14.07        63.35       110.99        44.19        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 
        2.63        61.61        65.23         9.07        50.66        16.93 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-4133 
       39.32         1.12        26.43        33.90         4.01         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 
        6.81         0.39        37.58        21.70       133.25       111.35 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 
      102.18        60.53        68.38        55.56        39.12        33.11 
TCGA-43-6647 TCGA-43-6773 TCGA-43-A475 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
       24.89         3.81         9.73         9.83         4.44        10.65 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-56-5898 TCGA-56-7223 
        0.39        29.95         5.46        30.35        18.25        14.53 
TCGA-56-7579 TCGA-56-7582 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A62T TCGA-58-8386 
       31.27        19.76        20.94        13.32        14.47         0.03 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2704 
       16.47        34.78        34.36        35.24        29.92        37.94 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
       92.71        80.45        49.48        56.91        50.33        42.64 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
       29.85        35.90        11.77        52.67        70.13        70.42 
TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MW TCGA-66-2734 
      102.67        59.97        45.57        89.29        53.88        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 
        2.01        21.07         0.92        21.01         0.99         1.02 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2782 
        2.01        23.01        19.00         2.01        12.03        12.00 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
        1.97        40.01         5.03        30.02        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-70-6722 TCGA-70-6723 TCGA-77-6845 TCGA-77-7141 
       49.05         2.73        12.07        12.33        23.28         0.49 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 
        0.16        46.78        32.55         6.51        55.73        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
      156.66        53.92        26.40        66.51        54.41        65.49 
TCGA-77-8156 TCGA-77-A5G8 TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       36.36        61.94         9.67        40.24         6.41        36.53 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
        1.15        18.94        19.04        24.13        31.56        30.64 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8352 TCGA-85-8354 TCGA-85-8666 TCGA-85-A4CN 
       34.52        10.09         5.29        32.71        22.59        34.13 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       30.48        19.73        27.16        15.29        29.92        12.39 
TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 
        3.65        11.77        20.22        22.62        10.59         3.48 
TCGA-94-A5I6 TCGA-96-8169 TCGA-96-A4JL TCGA-98-8023 TCGA-98-A538 TCGA-98-A53I 
       17.69        18.31        27.68        21.34        27.16        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NK-A5CR TCGA-O2-A52N 
       64.54        57.30         2.89        25.32        83.57        33.07 
TCGA-O2-A52Q 
        3.72 

$`7Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 TCGA-33-4532 
       12.20         4.80        31.99        27.19        14.93       129.01 
TCGA-33-6737 TCGA-34-2604 TCGA-39-5039 TCGA-43-2578 TCGA-43-7658 TCGA-43-8118 
       19.76        31.50        17.88        22.49        78.18         2.93 
TCGA-56-8201 TCGA-56-8305 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2712 
       13.05         3.45        17.85        21.04         3.58         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 
       35.34        32.32        66.61        20.78        30.81         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-98-8020 
       14.07        21.04         0.16        18.38        16.14         2.76 
TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NK-A5CT 
        5.69        21.21        19.10         0.07        39.85        65.65 
TCGA-NK-A5D1 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 
       16.80        92.15        92.42        86.96         2.79        49.94 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1078 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
       46.88        99.16        15.58       122.43       119.80        43.23 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       31.63        41.69        33.93        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1016 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       64.21        27.02        34.75        19.30         9.57        11.77 
TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
       14.63        71.34        79.20        11.74        30.12        62.86 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-A4WN 
       79.53       173.82       103.53       151.27        54.44         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2608 TCGA-34-5232 
        0.30        36.62         6.94       118.36        32.88        81.24 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 
       74.66        60.30        44.75         4.96        38.79         4.04 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 
        0.43         0.39         7.96         8.12         7.46         3.39 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
      126.58        68.58        55.20        82.52         1.71        24.33 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
        1.94        36.39        71.18        17.06        40.21        38.66 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 
       27.91        22.98        21.47         5.46        19.59        13.38 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-6026 
       11.77        14.20        13.32        12.16        13.02        13.91 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        0.39        28.34         8.75        27.45        28.96        12.43 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
       21.90        18.48        30.41         6.51         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       33.24        14.96         4.93         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 
       20.25        15.81        19.23        18.74         0.26        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46L TCGA-60-2695 
       13.55        29.95        71.24        85.12        56.65        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 TCGA-60-2710 TCGA-60-2716 
       12.23        10.22        96.82        21.93        66.54        48.49 
TCGA-60-2720 TCGA-60-2724 TCGA-60-2725 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG 
        3.19        23.57        26.83        68.15        55.30        70.62 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT 
       58.65        14.99        11.34        25.28        78.28        16.37 
TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       36.16        34.59        16.96         0.99         1.02         2.01 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 
        0.99        43.99        25.05         2.01         2.01         7.07 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 
        3.02        19.00         3.98        24.95        25.97        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
        4.04        22.98        10.06         6.64         6.94        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 
       16.18        14.73        29.56        73.12        75.09        11.18 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8008 TCGA-77-8131 
      140.09        73.22        70.13       106.95        86.76        12.59 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
       39.09        17.72       104.09        11.54        27.39         6.97 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       60.53       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       27.62        38.86        41.39        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8071 TCGA-85-8287 TCGA-85-8288 
        1.38        29.95        25.15        26.79         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       22.45        16.77         3.09         2.01        15.39         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB 
       36.59        38.14        12.59        18.08        30.28        30.97 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-90-6837 
       19.86        24.36        16.21        15.85        14.96        24.92 
TCGA-90-7767 TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
        2.93         2.70         4.01         5.26         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8170 TCGA-98-7454 
        5.03        26.63        14.14        71.01        17.46        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       30.81        30.67        18.15         2.01        27.02        20.32 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO 
        4.54         1.22        13.74         4.21        49.28        43.92 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       14.73        26.43         3.65        12.72        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           156.66            173.82 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            25.32             19.86 
[1] "0.0 - 156.7 (25.3)" "0.1 - 173.8 (19.9)"
[1] "hr=" "1.2"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         2       29       69        1        28        44
  7Q GAIN WILD-TYPE       0       60       83        1        37        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  7Q GAIN MUTATED           1         31          8        5
  7Q GAIN WILD-TYPE         2         32         11        2
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                29                60
  STAGE IB                69                83
  STAGE II                 1                 1
  STAGE IIA               28                37
  STAGE IIB               44                51
  STAGE III                1                 2
  STAGE IIIA              31                32
  STAGE IIIB               8                11
  STAGE IV                 5                 2
[1] 10  2
[1] 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    39 137  35   9
  7Q GAIN WILD-TYPE  73 157  36  15
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              39                73
  T2             137               157
  T3              35                36
  T4               9                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
  7Q GAIN MUTATED   130  65  20   2
  7Q GAIN WILD-TYPE 187  68  20   3
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             130               187
  N1              65                68
  N2              20                20
  N3               2                 3
[1] 4 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   183   5
  7Q GAIN WILD-TYPE 228   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    183    5
  7Q GAIN WILD-TYPE  228    2
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             183               228
  1               5                 2
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    49 171
  7Q GAIN WILD-TYPE  81 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     49  171
  7Q GAIN WILD-TYPE   81  200
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              49                81
  MALE               171               200
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   167  27
  7Q GAIN WILD-TYPE 217  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    167   27
  7Q GAIN WILD-TYPE  217   26
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              167               217
  YES              27                26
[1] 2 2
[1] FALSE
D14V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                       7
  7Q GAIN WILD-TYPE                                     8
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  7Q GAIN MUTATED                                        1
  7Q GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                         0
  7Q GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                           212
  7Q GAIN WILD-TYPE                                                         267
D14V10, multiclass
                                                             clus
vv                                                            7Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             212
                                                             clus
vv                                                            7Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               267
[1] 4 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   175   6   1   8
  7Q GAIN WILD-TYPE 224   6   3  15
D14V13, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             175               224
  R1               6                 6
  R2               1                 3
  RX               8                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       8                        17   144
  7Q GAIN WILD-TYPE     1                        14   205
D14V14, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   8                 1
  BLACK OR AFRICAN AMERICAN              17                14
  WHITE                                 144               205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 141
  7Q GAIN WILD-TYPE   6 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  141
  7Q GAIN WILD-TYPE    6  176
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO             141               176
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    70  59
  8P GAIN WILD-TYPE 210 155
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              129               365 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               59               155 
$`8P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-5472 TCGA-22-A5C4 
        4.47       123.19         4.80        31.99        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-34-2605 TCGA-43-2578 TCGA-43-A56V 
      129.01       133.74        19.76        28.96        22.49        12.03 
TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-94-7943 TCGA-96-7545 TCGA-NC-A5HD 
        9.01        66.61         8.02        18.38        57.07         0.07 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3414 TCGA-18-3421 TCGA-21-1070 
        0.43         8.58       117.57        23.54        86.96       119.54 
TCGA-21-1075 TCGA-21-1079 TCGA-21-1082 TCGA-21-5783 TCGA-21-5784 TCGA-22-1011 
       70.16        31.73       119.80        88.11        41.69         1.74 
TCGA-22-4596 TCGA-22-5473 TCGA-22-5479 TCGA-22-5482 TCGA-22-5489 TCGA-33-4583 
        0.56        63.55        86.30        11.74        62.86       151.27 
TCGA-33-4587 TCGA-33-AASB TCGA-34-5231 TCGA-34-5232 TCGA-34-5239 TCGA-34-7107 
       54.44         6.94        65.23        81.24        60.30         1.12 
TCGA-34-A5IX TCGA-37-4132 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5019 TCGA-39-5022 
       33.90         7.46         3.39        37.58       111.35        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5034 TCGA-39-5040 TCGA-43-3920 
       82.52         1.71        24.33        36.39        17.06        33.11 
TCGA-43-5670 TCGA-43-6647 TCGA-52-7811 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 
       27.91        24.89         8.75         6.51         0.10         3.48 
TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-60-2695 TCGA-60-2706 
       20.94        18.74        14.47         0.03        21.11        92.71 
TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 
       80.45        50.33        42.64         3.19        29.85        26.83 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5ML TCGA-63-A5MR 
       52.67        70.13        55.30        70.62        45.57        89.29 
TCGA-63-A5MY TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 TCGA-66-2767 
       34.59        21.07         0.99         0.99         0.99         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2788 TCGA-66-2789 
        7.07        23.01         3.02         2.01        22.98         4.04 
TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-77-7139 TCGA-77-7141 
       10.06        49.05         6.64        13.35       140.09         0.49 
TCGA-77-7335 TCGA-77-7463 TCGA-77-8007 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 
       70.13        46.78         6.51        39.09        17.72        11.54 
TCGA-77-8143 TCGA-77-8150 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 
       26.40        54.41         5.92        38.86        41.39        32.91 
TCGA-85-8052 TCGA-85-8287 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-A510 
       24.13         0.76         7.76        36.59        18.08        15.85 
TCGA-85-A513 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 TCGA-96-8169 TCGA-98-8023 
       29.92        11.77        22.62         2.70        18.31        21.34 
TCGA-98-A53A TCGA-98-A53B TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NK-A5CR 
       18.15         2.01        12.89        16.11        13.41        83.57 
TCGA-NK-A5CX TCGA-O2-A52Q TCGA-XC-AA0X 
        3.65         3.72         0.20 

$`8P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 
       12.20         6.18        27.19        32.19        14.93        48.82 
TCGA-22-5471 TCGA-33-4589 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 
       60.66         1.55        31.50        31.27        17.88        18.38 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 
        7.76        78.18         2.93        11.61        19.99        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
        3.45        17.00        16.77        17.85        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA 
        3.58        41.42        35.34        32.32        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 
       30.81         9.50        14.07        21.04         0.16        16.14 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE 
       19.36         2.76         5.69        21.21        19.10        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3412 
       39.85        40.90        65.65        16.80        75.75        11.34 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       92.15        36.07        92.42         2.79       154.32        49.94 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 
       46.88        99.16        60.89        34.78        15.58       122.43 
TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
        9.34        43.23        31.63        33.93        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
        7.33         4.31        64.21        14.10        27.02        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       35.08        48.33        24.13        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5477 
       32.02        19.30         9.57        11.77        14.63        44.25 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 
        0.79        71.34        79.20        18.84        30.12        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
       16.64        97.94        79.53       173.82       103.53        14.07 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI 
       63.35         4.70         0.30        36.62       110.99        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5234 
      118.36        27.16         2.63        61.61        32.88        74.66 
TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
        9.07        50.66        16.93        44.75        39.32         4.96 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       38.79         4.04        26.43         4.01         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EN 
        7.96         8.12         7.82         6.81         0.39        21.70 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 TCGA-39-5030 TCGA-39-5031 
      133.25       126.58        68.58       102.18         1.94        60.53 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       68.38        71.18        55.56        40.21        38.66        39.12 
TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       22.98        21.47         5.46         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       11.77         9.73        14.20        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
        9.83         4.44        10.65        13.91         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 
       29.95        28.34         5.46        30.35        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       12.43        18.25        21.90        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
       30.41        19.76        17.49        33.24        14.96         4.93 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       26.89        14.07         1.35         1.81        22.75        13.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
       10.36         9.93        20.25        15.81        19.23        13.32 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.26        13.25        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       34.78        85.12        34.36        56.65        35.24        29.92 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 
       12.23        10.22        96.82        37.94        21.93        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 
       66.54        56.91        48.49        35.90        23.57        11.77 
TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM 
       70.42        68.15       102.67        58.65        59.97        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       11.34        25.28        78.28        16.37        36.16        53.88 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       16.96        43.10         2.01         1.02         2.01         0.92 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
       43.99        21.01        25.05         2.01         1.02         2.01 
TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
       19.00        19.00        12.03         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        1.97        25.97        40.01        22.98         5.03        30.02 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J 
       54.08         4.01         2.73         6.94        16.18        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 
       11.18        73.22       106.95         0.16        32.55        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 
       55.73        37.81       156.66        12.59        53.92       104.09 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
       27.39         6.97        66.51        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GF 
      126.18       132.36       150.25        22.29        61.94        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
        9.67        40.24         6.41        36.53        34.95        31.30 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        1.38         1.15        29.95        18.94        25.15        19.04 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 
       31.56        26.79        30.64        34.52        10.09        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       22.45        16.77         5.29         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       15.39        38.14        12.59        22.59        30.28        34.13 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       30.97        19.86        24.36        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       16.21        14.96        15.29        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
        2.93        20.22        10.59         3.48         4.01         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        2.30         4.01         5.03        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       71.01        17.46        27.68        21.44        30.81        30.67 
TCGA-98-A538 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-LA-A446 
       27.16        27.02        20.32        18.58        20.71        13.18 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       11.84         4.54        64.54         1.22        57.30        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.21         2.89        49.28        43.92        25.32        14.73 
TCGA-NC-A5HT TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       26.43        33.07        12.72        43.89        11.18 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.03              0.13 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           151.27            173.82 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            22.62             21.44 
[1] "0.0 - 151.3 (22.6)" "0.1 - 173.8 (21.4)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         1       18       42        1        11        23
  8P GAIN WILD-TYPE       1       71      110        1        54        72
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  8P GAIN MUTATED           1         18          9        4
  8P GAIN WILD-TYPE         2         45         10        3
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                18                71
  STAGE IB                42               110
  STAGE II                 1                 1
  STAGE IIA               11                54
  STAGE IIB               23                72
  STAGE III                1                 2
  STAGE IIIA              18                45
  STAGE IIIB               9                10
  STAGE IV                 4                 3
[1] 10  2
[1] 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    25  76  16  12
  8P GAIN WILD-TYPE  87 218  55  12
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              25                87
  T2              76               218
  T3              16                55
  T4              12                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
  8P GAIN MUTATED    83  30  11   2
  8P GAIN WILD-TYPE 234 103  29   3
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              83               234
  N1              30               103
  N2              11                29
  N3               2                 3
[1] 4 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   106   4
  8P GAIN WILD-TYPE 305   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    106    4
  8P GAIN WILD-TYPE  305    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             106               305
  1               4                 3
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    34  95
  8P GAIN WILD-TYPE  96 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     34   95
  8P GAIN WILD-TYPE   96  276
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              34                96
  MALE                95               276
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   104  10
  8P GAIN WILD-TYPE 280  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    104   10
  8P GAIN WILD-TYPE  280   43
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              104               280
  YES              10                43
[1] 2 2
[1] FALSE
D15V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                       2
  8P GAIN WILD-TYPE                                    13
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  8P GAIN MUTATED                                        1
  8P GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                         1
  8P GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                           125
  8P GAIN WILD-TYPE                                                         354
D15V10, multiclass
                                                             clus
vv                                                            8P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             125
                                                             clus
vv                                                            8P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D15V11, continuous
D15V12, continuous
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED   101   5   0   1
  8P GAIN WILD-TYPE 298   7   4  22
D15V13, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0             101               298
  R1               5                 7
  R2               0                 4
  RX               1                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       3                        12    80
  8P GAIN WILD-TYPE     6                        19   269
D15V14, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              12                19
  WHITE                                  80               269
[1] 3 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     3  81
  8P GAIN WILD-TYPE   5 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   81
  8P GAIN WILD-TYPE    5  236
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              81               236
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   136 117
  8Q GAIN WILD-TYPE 144  97
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              253               241 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              117                97 
$`8Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI 
        4.47       123.19         4.80        31.99         6.18        32.19 
TCGA-22-1017 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 
       48.82        64.93        22.06       129.01       133.74         1.55 
TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 
       19.76        28.96        31.27        22.49        18.38         7.76 
TCGA-43-8118 TCGA-43-A56V TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 TCGA-56-A5DR 
        2.93        12.03        13.05        17.00        16.77         0.13 
TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        9.01        66.61         8.02         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD 
       57.07        19.36         2.76         5.69        19.10         0.07 
TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       40.90         0.43         8.58       117.57        11.34        23.54 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-21-1070 TCGA-21-1075 TCGA-21-1079 
       36.07        92.42        86.96       119.54        70.16        31.73 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
        9.34       119.80        43.23        88.11        41.69        33.93 
TCGA-21-5787 TCGA-22-1011 TCGA-22-1016 TCGA-22-4596 TCGA-22-4605 TCGA-22-4609 
       10.82         1.74        27.02         0.56        32.02         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       11.77        63.55        14.63        44.25         0.79        86.30 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-33-4583 TCGA-33-4587 
       79.20        11.74        30.12        62.86       151.27        54.44 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-34-5231 TCGA-34-5232 TCGA-34-5239 
        6.94       110.99        44.19        65.23        81.24        60.30 
TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 
       16.93        39.32        38.79         4.04        33.90         0.43 
TCGA-37-4132 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 
        7.46         3.39        37.58       126.58       111.35        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 
       82.52         1.71        24.33        36.39        68.38        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
       40.21        38.66        33.11        27.91        24.89        21.47 
TCGA-43-A475 TCGA-46-3766 TCGA-46-3768 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
        9.73        12.16         9.83        30.35         8.75        28.96 
TCGA-56-5897 TCGA-56-6545 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8622 
       12.43        21.90         0.10        17.49         3.48         1.81 
TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       20.25        20.94        13.32        18.74         0.26        14.47 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46M 
        0.03        13.25        16.47        34.78        85.12        35.24 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       21.11        10.22        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       80.45        56.91        50.33        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 
       35.90        23.57        26.83        11.77        52.67        55.30 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MW 
       70.62        58.65        59.97        45.57        89.29        53.88 
TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 
       34.59        43.10        21.07         0.99         1.02         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 
        0.99        43.99         0.99         2.01         7.07        23.01 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2782 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        3.02         2.01        12.00        22.98         4.04        22.98 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I 
       30.02        10.06        49.05         6.64        13.35        16.18 
TCGA-70-6722 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       12.07        75.09       140.09         0.49        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 
        0.16        46.78        32.55         6.51        55.73        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
      156.66        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G6 
       11.54        26.40         6.97        66.51        54.41        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 
        5.92        61.94        38.86         9.67        41.39         6.41 
TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 TCGA-85-8052 TCGA-85-8287 TCGA-85-8350 
       32.91         1.15        18.94        24.13         0.76        22.45 
TCGA-85-8353 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        3.09         7.76        36.59        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
       22.59        30.97        19.86        30.48        19.73        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
       14.96        29.92         3.65         2.93        11.77        22.62 
TCGA-92-7340 TCGA-92-7341 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 
        2.70         3.48        14.14        17.69        18.31        17.46 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-L3-A4E7 
       30.67        21.34        27.16        18.15         2.01        12.89 
TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HK 
       16.11        13.41         4.54        64.54         1.22         4.21 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q 
       14.73        26.43        83.57         3.65        33.07         3.72 
TCGA-XC-AA0X 
        0.20 

$`8Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-5595 TCGA-22-1000 TCGA-22-5471 TCGA-34-2604 TCGA-39-5039 
       12.20        27.19        14.93        60.66        31.50        17.88 
TCGA-43-7658 TCGA-43-A474 TCGA-56-7221 TCGA-56-8305 TCGA-56-A4BY TCGA-56-A4ZJ 
       78.18        11.61        19.99         3.45        17.85        21.04 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA 
        3.58        41.42        35.34        32.32        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-98-A53D TCGA-NC-A5HE 
       30.81         9.50        14.07        21.04        21.21        76.80 
TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3415 TCGA-18-4086 
       39.85        65.65        16.80        75.75        92.15         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 
      154.32        49.94        46.88        99.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1080 TCGA-21-5782 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       15.58       122.43        31.63        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
       64.21        14.10        20.48        35.08        48.33        24.13 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-5480 TCGA-22-5483 
       38.17        34.75        13.12        19.30        71.34        18.84 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       56.32        16.64        97.94        79.53       173.82       103.53 
TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ 
       14.07        63.35         4.70         0.30        36.62       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5234 TCGA-34-5236 
       27.16         2.63        61.61        32.88        74.66         9.07 
TCGA-34-5240 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-3783 
       50.66        44.75         4.96         1.12        26.43         4.01 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        0.39         7.96         8.12         7.82         6.81         0.39 
TCGA-37-A5EN TCGA-39-5011 TCGA-39-5021 TCGA-39-5027 TCGA-39-5030 TCGA-39-5031 
       21.70       133.25        68.58       102.18         1.94        60.53 
TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6143 TCGA-43-6771 TCGA-43-6773 
       71.18        55.56        39.12        22.98         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3767 
       19.59        13.38        11.77        14.20        13.32        13.02 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        4.44        10.65        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 
       28.34         5.46        27.45        18.25        18.48        14.53 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 TCGA-56-8082 
       31.27        30.41        19.76         6.51        33.24        14.96 
TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 
        4.93        26.89        14.07         1.35        22.75        13.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-58-8388 TCGA-58-8390 
       10.36         9.93        15.81        19.23        13.55        29.95 
TCGA-58-8391 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46N TCGA-60-2697 TCGA-60-2709 
       71.24        34.36        56.65        29.92        12.23        49.48 
TCGA-60-2710 TCGA-60-2716 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB 
       66.54        48.49        70.13        70.42        68.15       102.67 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       14.99        11.34        25.28        78.28        16.37        36.16 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2754 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 
       16.96         2.01         2.01        21.01        25.05         2.01 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        1.02         2.01        19.00        19.00        12.03         3.98 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2791 TCGA-66-2794 
       24.95         1.97        25.97        40.01         5.03        54.08 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 
        4.01         2.73         6.94        14.73        12.33        29.56 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-8008 TCGA-77-8144 
       73.12        23.28        11.18        73.22        86.76        27.39 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       65.49        60.53        36.36       126.18       132.36       150.25 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
       27.62        40.24        36.53        34.95        31.30         1.38 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
       29.95        25.15        19.04        31.56        26.79        30.64 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
       34.52        10.09        13.22        16.77         5.29        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A50M 
        2.01        15.39        30.28        34.13        24.36        27.16 
TCGA-85-A50Z TCGA-85-A512 TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED TCGA-90-A59Q 
       16.21        15.29        12.39        24.92        20.22        10.59 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         5.26         2.30         4.01         5.03        26.63 
TCGA-96-7544 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-A53C TCGA-98-A53H 
       71.01        27.68        21.44        30.81        27.02        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HI TCGA-NC-A5HJ 
       18.58        20.71        13.18        11.84        57.30        13.74 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-O2-A52S TCGA-O2-A52V 
        2.89        49.28        43.92        25.32        12.72        43.89 
TCGA-O2-A5IB 
       11.18 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.03              0.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           156.66            173.82 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             21.9              21.7 
[1] "0.0 - 156.7 (21.9)" "0.3 - 173.8 (21.7)"
[1] "hr=" "1.2"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         2       39       75        0        26        58
  8Q GAIN WILD-TYPE       0       50       77        2        39        37
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  8Q GAIN MUTATED           1         37         11        6
  8Q GAIN WILD-TYPE         2         26          8        1
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                39                50
  STAGE IB                75                77
  STAGE II                 0                 2
  STAGE IIA               26                39
  STAGE IIB               58                37
  STAGE III                1                 2
  STAGE IIIA              37                26
  STAGE IIIB              11                 8
  STAGE IV                 6                 1
[1] 10  2
[1] 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    49 151  41  15
  8Q GAIN WILD-TYPE  63 143  30   9
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              49                63
  T2             151               143
  T3              41                30
  T4              15                 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
  8Q GAIN MUTATED   155  76  19   2
  8Q GAIN WILD-TYPE 162  57  21   3
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             155               162
  N1              76                57
  N2              19                21
  N3               2                 3
[1] 4 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   210   6
  8Q GAIN WILD-TYPE 201   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    210    6
  8Q GAIN WILD-TYPE  201    1
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             210               201
  1               6                 1
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    65 191
  8Q GAIN WILD-TYPE  65 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     65  191
  8Q GAIN WILD-TYPE   65  180
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              65                65
  MALE               191               180
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   204  25
  8Q GAIN WILD-TYPE 180  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    204   25
  8Q GAIN WILD-TYPE  180   28
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              204               180
  YES              25                28
[1] 2 2
[1] FALSE
D16V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                       6
  8Q GAIN WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  8Q GAIN MUTATED                                        2
  8Q GAIN WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                         1
  8Q GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                           247
  8Q GAIN WILD-TYPE                                                         232
D16V10, multiclass
                                                             clus
vv                                                            8Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             247
                                                             clus
vv                                                            8Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
D16V12, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   203   8   0  10
  8Q GAIN WILD-TYPE 196   4   4  13
D16V13, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             203               196
  R1               8                 4
  R2               0                 4
  RX              10                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       4                        22   171
  8Q GAIN WILD-TYPE     5                         9   178
D16V14, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              22                 9
  WHITE                                 171               178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     5 162
  8Q GAIN WILD-TYPE   3 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5  162
  8Q GAIN WILD-TYPE    3  155
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             162               155
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    33  27
  9P GAIN WILD-TYPE 247 187
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               60               434 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               27               187 
$`9P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-43-7658 
        4.47         4.80       129.01       133.74         1.55        78.18 
TCGA-56-8308 TCGA-60-2712 TCGA-68-8250 TCGA-77-A5GA TCGA-94-A5I4 TCGA-NC-A5HM 
       17.00         9.01         8.02        42.08        16.14        39.85 
TCGA-NC-A5HR TCGA-22-4604 TCGA-22-5481 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
       40.90        13.12        79.20       173.82       151.27        14.07 
TCGA-33-AASJ TCGA-34-5239 TCGA-34-5240 TCGA-34-7107 TCGA-37-3792 TCGA-37-4133 
      118.36        60.30        50.66         1.12         0.39         7.82 
TCGA-39-5030 TCGA-39-5036 TCGA-43-6143 TCGA-43-A475 TCGA-46-6025 TCGA-51-4079 
        1.94        71.18        22.98         9.73        10.65         0.39 
TCGA-52-7622 TCGA-58-8386 TCGA-60-2695 TCGA-60-2704 TCGA-60-2714 TCGA-60-2722 
       28.34         0.03        21.11        37.94        50.33        29.85 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-66-2744 TCGA-68-7755 TCGA-77-8007 
       59.97        45.57        25.28         0.99         2.73         6.51 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6561 
       53.92        39.09        54.41       150.25        27.62        40.24 
TCGA-85-7698 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8353 TCGA-90-7769 
       31.30        31.56        30.64        10.09         3.09        11.77 
TCGA-92-8064 TCGA-98-A53I TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-XC-AA0X 
        5.26        18.58        13.74         2.89        49.28         0.20 

$`9P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19        31.99         6.18        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-6737 
       14.93        48.82        60.66        64.93        22.06        19.76 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 
       31.50        28.96        31.27        17.88        22.49        18.38 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 
        7.76         2.93        11.61        12.03        19.99        13.05 
TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
        3.45        16.77        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GB 
       41.42        35.34        32.32        66.61        20.78        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7545 
        9.50        14.07        21.04         0.16        18.38        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       19.36         2.76         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       76.80        65.65        16.80         0.43         8.58        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
      117.57        11.34        23.54        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       86.96         2.79       154.32        49.94       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       99.16        70.16        60.89        34.78        15.58        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
      122.43         9.34       119.80        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       41.69        33.93        10.82        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       64.21         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 
       48.33        24.13         0.56        38.17        34.75        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       19.30         9.57        11.77        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        0.79        86.30        71.34        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       62.86        56.32        16.64        97.94        79.53       103.53 
TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       54.44        63.35         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
      110.99        44.19        27.16         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 
       65.23        81.24        74.66         9.07        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       39.32         4.96        38.79         4.04        26.43        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
        4.01         0.43         7.96         8.12         7.46         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 
        0.39         3.39        37.58        21.70       133.25       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      111.35        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 
       24.33        60.53        36.39        68.38        55.56        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
       40.21        38.66        39.12        33.11        27.91        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       21.47         5.46         3.81        19.59        13.38        11.77 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       14.20        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
       13.91         0.39        29.95         5.46        30.35         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
       27.45        28.96        12.43        18.25        21.90        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       14.53        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       17.49        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
        9.93        20.25        15.81        20.94        19.23        13.32 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       18.74         0.26        14.47        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       71.24        16.47        34.78        85.12        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 
       35.24        29.92        12.23        10.22        96.82        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 
       21.93        80.45        49.48        66.54        56.91        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       42.64         3.19        35.90        23.57        26.83        11.77 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       52.67        70.13        70.42        68.15        55.30       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS 
       70.62        58.65        14.99        11.34        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       16.37        36.16        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
        2.01        21.07         1.02         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
       43.99        21.01        25.05         0.99         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
        2.01         2.01         7.07        23.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        2.01        19.00        12.03         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1.97        25.97        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        6.64         6.94        13.35        16.18        14.73        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.33        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       46.78        32.55        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       12.59        17.72       104.09        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        6.97        66.51        65.49        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 
      132.36        22.29         5.92        61.94        38.86         9.67 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
       41.39         6.41        36.53        34.95        32.91         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1.15        29.95        18.94        25.15        19.04        24.13 
TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       26.79        34.52         0.76        13.22        22.45        16.77 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        5.29        32.71         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       38.14        12.59        18.08        22.59        30.28        34.13 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       30.97        19.86        24.36        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       16.21        15.85        14.96        15.29        29.92        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        3.65        24.92         2.93        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
        2.70         3.48         4.01         2.30         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
       26.63        14.14        17.69        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       27.68        21.44        30.81        30.67        21.34        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 
       18.15         2.01        27.02        20.32        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG 
       16.11        13.18        13.41        11.84         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        1.22        57.30         4.21        43.92        25.32        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       26.43        83.57         3.65        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB 
       43.89        11.18 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.03              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           173.82            156.66 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           24.130            21.585 
[1] "0.0 - 173.8 (24.1)" "0.1 - 156.7 (21.6)"
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         0        7       15        1         9        21
  9P GAIN WILD-TYPE       2       82      137        1        56        74
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  9P GAIN MUTATED           0          7          0        1
  9P GAIN WILD-TYPE         3         56         19        6
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 7                82
  STAGE IB                15               137
  STAGE II                 1                 1
  STAGE IIA                9                56
  STAGE IIB               21                74
  STAGE III                0                 3
  STAGE IIIA               7                56
  STAGE IIIB               0                19
  STAGE IV                 1                 6
[1] 10  2
[1] 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     9  43   8   2
  9P GAIN WILD-TYPE 103 251  63  22
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               9               103
  T2              43               251
  T3               8                63
  T4               2                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                 N0  N1  N2  N3
  9P GAIN MUTATED    30  28   2   0
  9P GAIN WILD-TYPE 287 105  38   5
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              30               287
  N1              28               105
  N2               2                38
  N3               0                 5
[1] 4 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    54   1
  9P GAIN WILD-TYPE 357   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     54    1
  9P GAIN WILD-TYPE  357    6
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              54               357
  1               1                 6
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    17  45
  9P GAIN WILD-TYPE 113 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     17   45
  9P GAIN WILD-TYPE  113  326
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              17               113
  MALE                45               326
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    50   5
  9P GAIN WILD-TYPE 334  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     50    5
  9P GAIN WILD-TYPE  334   48
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               50               334
  YES               5                48
[1] 2 2
[1] FALSE
D17V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED                                       4
  9P GAIN WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  9P GAIN MUTATED                                        0
  9P GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED                                         0
  9P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                            58
  9P GAIN WILD-TYPE                                                         421
D17V10, multiclass
                                                             clus
vv                                                            9P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              58
                                                             clus
vv                                                            9P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               421
[1] 4 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    48   2   0   4
  9P GAIN WILD-TYPE 351  10   4  19
D17V13, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              48               351
  R1               2                10
  R2               0                 4
  RX               4                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       2                         5    40
  9P GAIN WILD-TYPE     7                        26   309
D17V14, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               5                26
  WHITE                                  40               309
[1] 3 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     2  35
  9P GAIN WILD-TYPE   6 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   35
  9P GAIN WILD-TYPE    6  282
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              35               282
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    48  43
  9Q GAIN WILD-TYPE 232 171
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               91               403 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               43               171 
$`9Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-33-4533 TCGA-33-4589 TCGA-43-5668 
        4.47         4.80        31.99       133.74         1.55        18.38 
TCGA-43-7658 TCGA-56-8308 TCGA-60-2711 TCGA-77-A5GA TCGA-94-A5I4 TCGA-96-A4JK 
       78.18        17.00        41.42        42.08        16.14        19.36 
TCGA-NC-A5HR TCGA-18-3412 TCGA-21-1072 TCGA-21-1076 TCGA-22-0940 TCGA-22-0944 
       40.90        11.34        99.16        60.89        21.99         7.33 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5477 TCGA-22-5483 TCGA-33-4566 
       38.17        13.12        11.77        44.25        18.84       173.82 
TCGA-33-4583 TCGA-33-4586 TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-5239 
      151.27        14.07       118.36         2.63        61.61        60.30 
TCGA-34-7107 TCGA-37-3792 TCGA-37-4133 TCGA-37-A5EL TCGA-39-5030 TCGA-39-5036 
        1.12         0.39         7.82        37.58         1.94        71.18 
TCGA-43-3394 TCGA-43-6143 TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 
       39.12        22.98         9.73         9.83        10.65         0.39 
TCGA-52-7622 TCGA-52-7809 TCGA-56-7582 TCGA-56-A4BX TCGA-58-8386 TCGA-58-8391 
       28.34         5.46        19.76        13.32         0.03        71.24 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2704 TCGA-60-2710 TCGA-60-2722 TCGA-63-A5MJ 
       35.24        21.11        37.94        66.54        29.85        59.97 
TCGA-63-A5ML TCGA-63-A5MP TCGA-66-2744 TCGA-66-2757 TCGA-66-2770 TCGA-66-2792 
       45.57        25.28         0.99        43.99        23.01        30.02 
TCGA-68-7755 TCGA-77-7141 TCGA-77-7335 TCGA-77-7465 TCGA-77-8009 TCGA-77-8133 
        2.73         0.49        70.13        32.55        55.73        53.92 
TCGA-77-8136 TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5GF 
       39.09        27.39        54.41        65.49       150.25        27.62 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7844 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 
       36.53        31.30        29.95        31.56        30.64        10.09 
TCGA-85-8353 TCGA-85-8580 TCGA-85-A4CN TCGA-90-7769 TCGA-96-A4JL TCGA-98-A53I 
        3.09        36.59        34.13        11.77        27.68        18.58 
TCGA-98-A53J TCGA-L3-A524 TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NK-A5CR TCGA-O2-A52N 
       20.71        16.11        13.74         2.89        83.57        33.07 
TCGA-XC-AA0X 
        0.20 

$`9Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20       123.19         6.18        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-6737 
       48.82        60.66        64.93        22.06       129.01        19.76 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-7657 
       31.50        28.96        31.27        17.88        22.49         7.76 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
        2.93        11.61        12.03        19.99        13.05         3.45 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 
       16.77        17.85        21.04         0.13         3.58         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB 
       35.34        32.32        66.61         8.02        20.78        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7545 
        9.50        14.07        21.04         0.16        18.38        57.07 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE 
        2.76         5.69        21.21        19.10         0.07        76.80 
TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       39.85        65.65        16.80         0.43         8.58        75.75 
TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
      117.57        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
        2.79       154.32        49.94       119.54        46.88        70.16 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       34.78        15.58        31.73       122.43         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
       43.23        31.63        88.11        41.69        33.93        10.82 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
        4.31        64.21         1.74        14.10        27.02        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4605 
       35.08        48.33        24.13         0.56        34.75        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 
       19.30         9.57        63.55        14.63         0.79        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       71.34        79.20        11.74        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 
       16.64        97.94        79.53       103.53        54.44        63.35 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
        4.70         0.30        36.62         6.94       110.99        44.19 
TCGA-33-AASL TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       27.16        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 
       50.66        16.93        44.75        39.32         4.96        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
        4.04        26.43        33.90         4.01         0.43         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EN 
        8.12         7.46         6.81         0.39         3.39        21.70 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
      133.25       126.58       111.35        68.58        55.20        82.52 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
      102.18         1.71        24.33        60.53        36.39        68.38 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 
       55.56        17.06        40.21        38.66        33.11        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 
       11.77        14.20        13.32        12.16        13.02         4.44 
TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
       13.91         0.39        29.95        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 
       28.96        12.43        18.25        21.90        18.48        14.53 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       31.27        30.41         6.51         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       14.96         4.93         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75        13.81        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       15.81        20.94        19.23        18.74         0.26        14.47 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       13.25        13.55        29.95        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       34.36        56.65        29.92        12.23        10.22        96.82 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2713 TCGA-60-2714 
       92.71        21.93        80.45        49.48        56.91        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       48.49        42.64         3.19        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR 
      102.67        70.62        58.65        14.99        11.34        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        36.16        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       43.10         2.01        21.07         1.02         2.01         0.92 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
        0.99        21.01        25.05         0.99         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         2.01         7.07        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       25.97        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 
       10.06        54.08         4.01        49.05         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 
       13.35        16.18        14.73        12.07        12.33        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 
       73.12        75.09        23.28        11.18       140.09        73.22 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
      106.95         0.16        46.78         6.51        86.76        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
      156.66        12.59        17.72       104.09        11.54        26.40 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        6.97        66.51        60.53        36.36       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       22.29         5.92        61.94        38.86         9.67        41.39 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       40.24         6.41        34.95        32.91         1.38         1.15 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 
       18.94        25.15        19.04        24.13        26.79        34.52 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
        0.76        13.22        22.45        16.77         5.29        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        2.01        15.39         7.76        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       22.59        30.28        30.97        19.86        24.36        30.48 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
       19.73        27.16        16.21        15.85        14.96        15.29 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED 
       29.92        12.39         3.65        24.92         2.93        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       22.62        10.59         2.70         3.48         4.01         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        2.30         4.01         5.03        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       71.01        18.31        17.46        21.44        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       21.34        27.16        18.15         2.01        27.02        20.32 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG 
       12.89        13.18        13.41        11.84         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
        1.22        57.30         4.21        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       14.73        26.43         3.65         3.72        12.72        43.89 
TCGA-O2-A5IB 
       11.18 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.03              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           173.82            156.66 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            27.68             21.04 
[1] "0.0 - 173.8 (27.7)" "0.1 - 156.7 (21.0)"
[1] "hr=" "1"  
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         1       11       29        1        16        22
  9Q GAIN WILD-TYPE       1       78      123        1        49        73
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  9Q GAIN MUTATED           0          9          1        1
  9Q GAIN WILD-TYPE         3         54         18        6
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                11                78
  STAGE IB                29               123
  STAGE II                 1                 1
  STAGE IIA               16                49
  STAGE IIB               22                73
  STAGE III                0                 3
  STAGE IIIA               9                54
  STAGE IIIB               1                18
  STAGE IV                 1                 6
[1] 10  2
[1] 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    17  60  11   3
  9Q GAIN WILD-TYPE  95 234  60  21
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              17                95
  T2              60               234
  T3              11                60
  T4               3                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                 N0  N1  N2  N3
  9Q GAIN MUTATED    52  34   4   0
  9Q GAIN WILD-TYPE 265  99  36   5
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              52               265
  N1              34                99
  N2               4                36
  N3               0                 5
[1] 4 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    82   1
  9Q GAIN WILD-TYPE 329   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     82    1
  9Q GAIN WILD-TYPE  329    6
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              82               329
  1               1                 6
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    26  65
  9Q GAIN WILD-TYPE 104 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     26   65
  9Q GAIN WILD-TYPE  104  306
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              26               104
  MALE                65               306
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    72   9
  9Q GAIN WILD-TYPE 312  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     72    9
  9Q GAIN WILD-TYPE  312   44
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               72               312
  YES               9                44
[1] 2 2
[1] FALSE
D18V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED                                       4
  9Q GAIN WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  9Q GAIN MUTATED                                        0
  9Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED                                         0
  9Q GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                            87
  9Q GAIN WILD-TYPE                                                         392
D18V10, multiclass
                                                             clus
vv                                                            9Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              87
                                                             clus
vv                                                            9Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               392
[1] 4 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    76   2   0   2
  9Q GAIN WILD-TYPE 323  10   4  21
D18V13, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              76               323
  R1               2                10
  R2               0                 4
  RX               2                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       3                         5    63
  9Q GAIN WILD-TYPE     6                        26   286
D18V14, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               5                26
  WHITE                                  63               286
[1] 3 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     2  56
  9Q GAIN WILD-TYPE   6 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   56
  9Q GAIN WILD-TYPE    6  261
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              56               261
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    41  37
  10P GAIN WILD-TYPE 239 177
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                78                416 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                37                177 
$`10P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-22-1017 TCGA-33-6737 TCGA-34-2609 TCGA-43-5668 
        4.47        31.99        48.82        19.76        31.27        18.38 
TCGA-56-8201 TCGA-56-A5DR TCGA-60-2712 TCGA-94-7943 TCGA-96-7545 TCGA-NK-A7XE 
       13.05         0.13         9.01        18.38        57.07         0.43 
TCGA-O2-A52W TCGA-18-3417 TCGA-21-1070 TCGA-21-1083 TCGA-21-5783 TCGA-21-5787 
        8.58        36.07       119.54        43.23        88.11        10.82 
TCGA-22-0944 TCGA-22-5473 TCGA-33-4566 TCGA-33-AASB TCGA-33-AASI TCGA-34-5928 
        7.33        63.55       173.82         6.94        44.19        39.32 
TCGA-34-7107 TCGA-37-4133 TCGA-37-4141 TCGA-43-3394 TCGA-43-5670 TCGA-46-6025 
        1.12         7.82         0.39        39.12        27.91        10.65 
TCGA-52-7811 TCGA-56-7222 TCGA-56-8304 TCGA-56-A4BX TCGA-58-A46L TCGA-60-2698 
        8.75        18.48         3.48        13.32        56.65        10.22 
TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-A5MG TCGA-66-2756 TCGA-66-2763 
       23.57        11.77        52.67        70.62         0.99         0.99 
TCGA-66-2778 TCGA-66-2782 TCGA-66-2792 TCGA-77-7142 TCGA-77-7463 TCGA-77-8143 
       19.00        12.00        30.02        73.22        46.78        26.40 
TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-85-6560 
       66.51        54.41       132.36         5.92        61.94        41.39 
TCGA-85-6561 TCGA-85-7843 TCGA-85-8350 TCGA-85-8352 TCGA-85-8582 TCGA-85-A4JB 
       40.24         1.15        22.45         5.29        38.14        30.97 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED TCGA-94-A4VJ 
       27.16        15.85        12.39         2.93        20.22        14.14 
TCGA-98-8022 TCGA-98-A53B TCGA-98-A53I TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL 
       30.67         2.01        18.58        64.54        57.30         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
       49.28        25.32        14.73        26.43        83.57         3.65 

$`10P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19         4.80         6.18        27.19        32.19 
TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       14.93        60.66        64.93        22.06       129.01       133.74 
TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-7657 
        1.55        31.50        28.96        17.88        22.49         7.76 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 
       78.18         2.93        11.61        12.03        19.99         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 
       17.00        16.77        17.85        21.04         3.58        41.42 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
       35.34        32.32        66.61         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 
       30.81         9.50        14.07        21.04         0.16        16.14 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       19.36         2.76         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 
       76.80        39.85        40.90        65.65        16.80        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 
      117.57        11.34        23.54        92.15        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2.79       154.32        49.94        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       60.89        34.78        15.58        31.73       122.43         9.34 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-1002 
      119.80        31.63        41.69        33.93        21.99         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       64.21         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       48.33        24.13         0.56        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5477 
       32.02        19.30         9.57        11.77        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
        0.79        86.30        71.34        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 
       30.12        62.86        56.32        16.64        97.94        79.53 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
        0.30        36.62       110.99       118.36        27.16         2.63 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       61.61        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       60.30        50.66        16.93        44.75         4.96        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
        4.04        26.43        33.90         4.01         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL 
        7.96         8.12         7.46         6.81         3.39        37.58 
TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
       21.70       133.25       126.58       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       36.39        68.38        71.18        55.56        17.06        40.21 
TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       38.66        33.11        22.98        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        3.81        19.59        13.38        11.77         9.73        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6026 
       13.32        12.16        13.02         9.83         4.44        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
        0.39         0.39        29.95        28.34         5.46        30.35 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 
       27.45        28.96        12.43        18.25        21.90        14.53 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
       31.27        30.41        19.76         6.51         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       33.24        14.96         4.93        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75        13.81        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       15.81        20.94        19.23        18.74         0.26        14.47 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.03        13.25        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       34.78        85.12        34.36        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       12.23        96.82        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       49.48        66.54        56.91        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 
        3.19        29.85        35.90        26.83        70.13        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
       68.15        55.30       102.67        58.65        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       14.99        11.34        25.28        89.29        78.28        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
       36.16        53.88        34.59        16.96        43.10         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
       21.07         0.99         1.02         2.01         0.92        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       21.01        25.05         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 
        7.07        23.01        19.00         3.02         2.01        12.03 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        3.98        24.95         1.97        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
        4.04        22.98         5.03        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
       49.05         2.73         6.64         6.94        13.35        16.18 
TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       14.73        12.07        12.33        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       23.28        11.18       140.09         0.49        70.13       106.95 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
        0.16        32.55         6.51        86.76        55.73        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
      156.66        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
       11.54        27.39         6.97        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
      126.18       150.25        22.29        27.62        38.86         9.67 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
        6.41        36.53        34.95        31.30        32.91         1.38 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       29.95        18.94        25.15        19.04        24.13        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       26.79        30.64        34.52        10.09         0.76        13.22 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         3.09        32.71         2.01        15.39         7.76 
TCGA-85-8580 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       36.59        12.59        18.08        22.59        30.28        34.13 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 
       19.86        24.36        30.48        19.73        16.21        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4EE 
       15.29        29.92         3.65        24.92        11.77        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       10.59         2.70         3.48         4.01         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        4.01         5.03        26.63        17.69        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 
       17.46        27.68        21.44        30.81        21.34        27.16 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 
       18.15        27.02        20.32        20.71        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ 
       13.18        13.41        11.84         4.54         1.22        13.74 
TCGA-NC-A5HK TCGA-NC-A5HO TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
        4.21        43.92        33.07         3.72        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.13               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            173.82             156.66 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            21.335             21.800 
[1] "0.1 - 173.8 (21.3)" "0.0 - 156.7 (21.8)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         1       12       17        1        13        14
  10P GAIN WILD-TYPE       1       77      135        1        52        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  10P GAIN MUTATED           0         14          3        2
  10P GAIN WILD-TYPE         3         49         16        5
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 12                 77
  STAGE IB                 17                135
  STAGE II                  1                  1
  STAGE IIA                13                 52
  STAGE IIB                14                 81
  STAGE III                 0                  3
  STAGE IIIA               14                 49
  STAGE IIIB                3                 16
  STAGE IV                  2                  5
[1] 10  2
[1] 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    14  48  13   3
  10P GAIN WILD-TYPE  98 246  58  21
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               14                 98
  T2               48                246
  T3               13                 58
  T4                3                 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                  N0  N1  N2  N3
  10P GAIN MUTATED    45  23   7   1
  10P GAIN WILD-TYPE 272 110  33   4
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               45                272
  N1               23                110
  N2                7                 33
  N3                1                  4
[1] 4 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    63   2
  10P GAIN WILD-TYPE 348   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     63    2
  10P GAIN WILD-TYPE  348    5
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               63                348
  1                2                  5
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    12  66
  10P GAIN WILD-TYPE 118 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12   66
  10P GAIN WILD-TYPE  118  305
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               12                118
  MALE                 66                305
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    60   7
  10P GAIN WILD-TYPE 324  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     60    7
  10P GAIN WILD-TYPE  324   46
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                60                324
  YES                7                 46
[1] 2 2
[1] FALSE
D19V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                       2
  10P GAIN WILD-TYPE                                    13
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  10P GAIN MUTATED                                        0
  10P GAIN WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                         0
  10P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                            76
  10P GAIN WILD-TYPE                                                         403
D19V10, multiclass
                                                             clus
vv                                                            10P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               76
                                                             clus
vv                                                            10P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                403
[1] 4 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    62   0   1   2
  10P GAIN WILD-TYPE 337  12   3  21
D19V13, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               62                337
  R1                0                 12
  R2                1                  3
  RX                2                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       3                         8    51
  10P GAIN WILD-TYPE     6                        23   298
D19V14, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                8                 23
  WHITE                                   51                298
[1] 3 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     1  50
  10P GAIN WILD-TYPE   7 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   50
  10P GAIN WILD-TYPE    7  267
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               50                267
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    23  21
  10Q GAIN WILD-TYPE 257 193
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                44                450 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                21                193 
$`10Q GAIN MUTATED`
TCGA-18-3416 TCGA-34-2609 TCGA-56-8201 TCGA-56-A5DR TCGA-94-7943 TCGA-NK-A7XE 
       31.99        31.27        13.05         0.13        18.38         0.43 
TCGA-21-1070 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-5473 TCGA-33-4566 
      119.54        43.23        33.93        10.82        63.55       173.82 
TCGA-33-4582 TCGA-33-AASI TCGA-34-5241 TCGA-34-5928 TCGA-37-4141 TCGA-43-5670 
      103.53        44.19        16.93        39.32         0.39        27.91 
TCGA-52-7811 TCGA-56-7222 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-77-7142 
        8.75        18.48        23.57        11.77        52.67        73.22 
TCGA-77-8130 TCGA-77-8150 TCGA-77-A5G7 TCGA-85-6561 TCGA-85-7843 TCGA-85-8350 
      156.66        54.41         5.92        40.24         1.15        22.45 
TCGA-85-8352 TCGA-85-A50M TCGA-85-A510 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED 
        5.29        27.16        15.85        12.39         2.93        20.22 
TCGA-94-A4VJ TCGA-98-A53B TCGA-98-A53I TCGA-NC-A5HG TCGA-NC-A5HL TCGA-NC-A5HP 
       14.14         2.01        18.58        64.54         2.89        25.32 
TCGA-NC-A5HQ TCGA-NK-A5CX 
       14.73         3.65 

$`10Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19         4.80         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
      129.01       133.74         1.55        19.76        31.50        28.96 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       17.88        22.49        18.38         7.76        78.18         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       11.61        12.03        19.99         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.85        21.04         3.58        41.42         9.01        35.34 
TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       32.32        66.61         8.02        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-7545 
        9.50        14.07        21.04         0.16        16.14        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       19.36         2.76         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W 
       76.80        39.85        40.90        65.65        16.80         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
       75.75       117.57        11.34        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 
       92.42        86.96         2.79       154.32        49.94        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       99.16        70.16        60.89        34.78        15.58        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
      122.43         9.34       119.80        31.63        88.11        41.69 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       21.99         7.33         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       27.02        20.48        35.08        48.33        24.13         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       38.17        34.75        13.12        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       11.77        14.63        44.25         0.79        86.30        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       16.64        97.94        79.53       151.27        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       63.35         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
      118.36        27.16         2.63        61.61        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
       81.24        74.66         9.07        60.30        50.66        44.75 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
        4.96         1.12        38.79         4.04        26.43        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        4.01         0.43         0.39         7.96         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        7.82         6.81         3.39        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1.71        24.33         1.94        60.53        36.39        68.38 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       71.18        55.56        17.06        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       33.11        22.98        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
       19.59        13.38        11.77         9.73        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       12.16        13.02         9.83         4.44        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
        0.39         0.39        29.95        28.34         5.46        30.35 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 
       27.45        28.96        12.43        18.25        21.90        14.53 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
       31.27        30.41        19.76         6.51         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       33.24        14.96         4.93         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK 
       20.25        15.81        20.94        19.23        13.32        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26        14.47         0.03        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       71.24        16.47        34.78        85.12        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       35.24        29.92        21.11        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       56.91        50.33        48.49        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       35.90        26.83        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       11.34        25.28        89.29        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       53.88        34.59        16.96        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        0.99         1.02         2.01         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         7.07        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       25.97        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
       30.02        10.06        54.08         4.01        49.05         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        6.64         6.94        13.35        16.18        14.73        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.33        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
      140.09         0.49        70.13       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 
       32.55         6.51        86.76        55.73        37.81        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       53.92        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
       27.39         6.97        66.51        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GF 
      126.18       132.36       150.25        22.29        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       38.86         9.67        41.39         6.41        36.53        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       31.30        32.91         1.38        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       19.04        24.13        31.56        26.79        30.64        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
       10.09         0.76        13.22        16.77         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01        15.39         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
       18.08        22.59        30.28        34.13        30.97        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
       24.36        30.48        19.73        16.21        14.96        15.29 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
       29.92         3.65        24.92        11.77        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
        2.70         3.48         4.01         5.26         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        5.03        26.63        17.69        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       27.68        21.44        30.81        30.67        21.34        27.16 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 
       18.15        27.02        20.32        20.71        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI 
       13.18        13.41        11.84         4.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CR 
       13.74         4.21        49.28        43.92        26.43        83.57 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         3.72        12.72        43.89        11.18         0.20 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.13               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            173.82             154.32 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            19.400             21.915 
[1] "0.1 - 173.8 (19.4)" "0.0 - 154.3 (21.9)"
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         0        8        9        0         9         8
  10Q GAIN WILD-TYPE       2       81      143        2        56        87
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  10Q GAIN MUTATED           0          7          1        1
  10Q GAIN WILD-TYPE         3         56         18        6
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  8                 81
  STAGE IB                  9                143
  STAGE II                  0                  2
  STAGE IIA                 9                 56
  STAGE IIB                 8                 87
  STAGE III                 0                  3
  STAGE IIIA                7                 56
  STAGE IIIB                1                 18
  STAGE IV                  1                  6
[1] 10  2
[1] 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     8  28   7   1
  10Q GAIN WILD-TYPE 104 266  64  23
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                8                104
  T2               28                266
  T3                7                 64
  T4                1                 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                  N0  N1  N2  N3
  10Q GAIN MUTATED    25  13   4   0
  10Q GAIN WILD-TYPE 292 120  36   5
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               25                292
  N1               13                120
  N2                4                 36
  N3                0                  5
[1] 4 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    36   1
  10Q GAIN WILD-TYPE 375   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     36    1
  10Q GAIN WILD-TYPE  375    6
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               36                375
  1                1                  6
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     7  37
  10Q GAIN WILD-TYPE 123 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7   37
  10Q GAIN WILD-TYPE  123  334
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                7                123
  MALE                 37                334
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    34   6
  10Q GAIN WILD-TYPE 350  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     34    6
  10Q GAIN WILD-TYPE  350   47
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                34                350
  YES                6                 47
[1] 2 2
[1] FALSE
D20V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED                                       1
  10Q GAIN WILD-TYPE                                    14
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  10Q GAIN MUTATED                                        0
  10Q GAIN WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED                                         0
  10Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                            43
  10Q GAIN WILD-TYPE                                                         436
D20V10, multiclass
                                                             clus
vv                                                            10Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               43
                                                             clus
vv                                                            10Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                436
[1] 4 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    35   0   0   1
  10Q GAIN WILD-TYPE 364  12   4  22
D20V13, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               35                364
  R1                0                 12
  R2                0                  4
  RX                1                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       2                         5    32
  10Q GAIN WILD-TYPE     7                        26   317
D20V14, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                5                 26
  WHITE                                   32                317
[1] 3 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  33
  10Q GAIN WILD-TYPE   7 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   33
  10Q GAIN WILD-TYPE    7  284
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               33                284
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    44  31
  11P GAIN WILD-TYPE 236 183
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                75                419 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                183 
$`11P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 TCGA-43-A474 
        4.47         4.80        22.49        18.38        78.18        11.61 
TCGA-56-8305 TCGA-56-8308 TCGA-77-A5GB TCGA-94-7943 TCGA-96-A4JK TCGA-NC-A5HM 
        3.45        17.00        30.81        18.38        19.36        39.85 
TCGA-NK-A7XE TCGA-21-1070 TCGA-21-1072 TCGA-21-1079 TCGA-21-5783 TCGA-22-4591 
        0.43       119.54        99.16        31.73        88.11        20.48 
TCGA-22-4594 TCGA-22-4595 TCGA-22-5491 TCGA-33-4582 TCGA-33-4583 TCGA-34-5239 
       48.33        24.13        56.32       103.53       151.27        60.30 
TCGA-34-8456 TCGA-39-5027 TCGA-39-5029 TCGA-39-5034 TCGA-39-5036 TCGA-43-5670 
       26.43       102.18        24.33        36.39        71.18        27.91 
TCGA-43-6771 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-6545 
        5.46        13.91         5.46        30.35        28.96        21.90 
TCGA-56-7730 TCGA-56-A49D TCGA-56-A4BX TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
        6.51        20.94        13.32        42.64         3.19        29.85 
TCGA-63-7020 TCGA-63-A5MI TCGA-66-2734 TCGA-66-2744 TCGA-66-2765 TCGA-66-2766 
       70.13        58.65        43.10         0.99         2.01         1.02 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2785 TCGA-66-2791 TCGA-68-7755 TCGA-70-6723 
       23.01         2.01         1.97         5.03         2.73        12.33 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-7463 TCGA-77-8007 
       29.56        23.28        11.18        73.22        46.78         6.51 
TCGA-77-8139 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-6560 
      104.09       132.36       150.25        22.29         5.92        41.39 
TCGA-85-8276 TCGA-90-7767 TCGA-90-A4EE TCGA-92-8064 TCGA-96-8169 TCGA-98-A53B 
       34.52         2.93        22.62         5.26        18.31         2.01 
TCGA-NC-A5HH TCGA-NC-A5HL TCGA-O2-A52S 
        1.22         2.89        12.72 

$`11P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19        31.99         6.18        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       14.93        48.82        60.66        64.93        22.06       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      133.74         1.55        19.76        31.50        28.96        31.27 
TCGA-39-5039 TCGA-43-7657 TCGA-43-8118 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 
       17.88         7.76         2.93        12.03        19.99        13.05 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       16.77        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
        9.01        35.34        32.32        66.61         8.02        20.78 
TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 
       42.08         9.50        14.07        21.04         0.16        16.14 
TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       57.07         2.76         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 
       76.80        40.90        65.65        16.80         8.58        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
      117.57        11.34        23.54        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1075 
       86.96         2.79       154.32        49.94        46.88        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       60.89        34.78        15.58       122.43         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
       43.23        31.63        41.69        33.93        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        7.33         4.31        64.21         1.74        14.10        27.02 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       35.08         0.56        38.17        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       19.30         9.57        11.77        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
        0.79        86.30        71.34        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       30.12        62.86        16.64        97.94        79.53       173.82 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       14.07        54.44        63.35         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
        6.94       110.99        44.19       118.36        27.16         2.63 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       61.61        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       50.66        16.93        44.75        39.32         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       38.79         4.04        33.90         4.01         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        7.96         8.12         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        3.39        37.58        21.70       133.25       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 
       68.58        55.20        82.52         1.71         1.94        60.53 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       68.38        55.56        17.06        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 
       33.11        22.98        24.89        21.47         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
       13.02         9.83         4.44        10.65         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 
       29.95        28.34         8.75        27.45        12.43        18.25 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 
       18.48        14.53        31.27        30.41        19.76         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       17.49        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS 
        9.93        20.25        15.81        19.23        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
       14.47         0.03        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       16.47        34.78        85.12        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       29.92        21.11        12.23        10.22        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       92.71        21.93        80.45        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       50.33        48.49        35.90        23.57        26.83        11.77 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG 
       52.67        70.42        68.15        55.30       102.67        70.62 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       59.97        45.57        14.99        11.34        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        36.16        53.88        34.59        16.96 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
        2.01        21.07         1.02         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 
       43.99        21.01        25.05         0.99         2.01         2.01 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        7.07        19.00         3.02        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       12.00        24.95        25.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
       22.98        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        6.64         6.94        13.35        16.18        14.73        12.07 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       73.12        75.09       140.09         0.49        70.13       106.95 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        0.16        32.55        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 
       12.59        53.92        39.09        17.72        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       27.39         6.97        66.51        54.41        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       36.36       126.18        61.94        27.62        38.86         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       40.24         6.41        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        1.38         1.15        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 
       24.13        31.56        26.79        30.64        10.09         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       13.22        22.45        16.77         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01        15.39         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
       18.08        22.59        30.28        34.13        30.97        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        30.48        19.73        27.16        16.21        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       14.96        15.29        29.92        12.39         3.65        24.92 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       11.77        20.22        10.59         2.70         3.48         4.01 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        2.30         4.01         5.03        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       71.01        17.46        27.68        21.44        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       21.34        27.16        18.15        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN 
        4.54        64.54        57.30        13.74         4.21        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
       43.92        25.32        14.73        26.43        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         3.72        43.89        11.18         0.20 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.43               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            151.27             173.82 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             22.49              21.44 
[1] "0.4 - 151.3 (22.5)" "0.0 - 173.8 (21.4)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         0       10       23        0        13        13
  11P GAIN WILD-TYPE       2       79      129        2        52        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  11P GAIN MUTATED           1         12          2        0
  11P GAIN WILD-TYPE         2         51         17        7
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 10                 79
  STAGE IB                 23                129
  STAGE II                  0                  2
  STAGE IIA                13                 52
  STAGE IIB                13                 82
  STAGE III                 1                  2
  STAGE IIIA               12                 51
  STAGE IIIB                2                 17
  STAGE IV                  0                  7
[1] 10  2
[1] 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    16  43  13   3
  11P GAIN WILD-TYPE  96 251  58  21
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               16                 96
  T2               43                251
  T3               13                 58
  T4                3                 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                  N0  N1  N2  N3
  11P GAIN MUTATED    47  15  10   1
  11P GAIN WILD-TYPE 270 118  30   4
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               47                270
  N1               15                118
  N2               10                 30
  N3                1                  4
[1] 4 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    65   0
  11P GAIN WILD-TYPE 346   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     65    0
  11P GAIN WILD-TYPE  346    7
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               65                346
  1                0                  7
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    15  60
  11P GAIN WILD-TYPE 115 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     15   60
  11P GAIN WILD-TYPE  115  311
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               15                115
  MALE                 60                311
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    53   8
  11P GAIN WILD-TYPE 331  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     53    8
  11P GAIN WILD-TYPE  331   45
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                53                331
  YES                8                 45
[1] 2 2
[1] FALSE
D21V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED                                       2
  11P GAIN WILD-TYPE                                    13
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  11P GAIN MUTATED                                        1
  11P GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED                                         0
  11P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                            72
  11P GAIN WILD-TYPE                                                         407
D21V10, multiclass
                                                             clus
vv                                                            11P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               72
                                                             clus
vv                                                            11P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                407
[1] 4 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    58   3   1   3
  11P GAIN WILD-TYPE 341   9   3  20
D21V13, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               58                341
  R1                3                  9
  R2                1                  3
  RX                3                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       2                         2    51
  11P GAIN WILD-TYPE     7                        29   298
D21V14, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                2                 29
  WHITE                                   51                298
[1] 3 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  39
  11P GAIN WILD-TYPE   7 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   39
  11P GAIN WILD-TYPE    7  278
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               39                278
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    55  34
  11Q GAIN WILD-TYPE 225 180
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                89                405 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                34                180 
$`11Q GAIN MUTATED`
TCGA-18-3410 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 TCGA-56-8305 TCGA-56-8308 
        4.80        22.49        18.38        78.18         3.45        17.00 
TCGA-56-A5DR TCGA-77-A5GB TCGA-94-7943 TCGA-96-A4JK TCGA-NC-A5HM TCGA-NC-A5HR 
        0.13        30.81        18.38        19.36        39.85        40.90 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1079 TCGA-21-5786 TCGA-22-4591 TCGA-22-4594 
      119.54        99.16        31.73        33.93        20.48        48.33 
TCGA-22-4595 TCGA-22-5491 TCGA-33-4582 TCGA-33-4583 TCGA-33-AASD TCGA-34-5231 
       24.13        56.32       103.53       151.27       110.99        65.23 
TCGA-34-8455 TCGA-34-8456 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        4.04        26.43         7.46         6.81         0.39         3.39 
TCGA-39-5011 TCGA-39-5029 TCGA-39-5034 TCGA-39-5036 TCGA-43-5670 TCGA-43-6143 
      133.25        24.33        36.39        71.18        27.91        22.98 
TCGA-43-6771 TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7730 
        5.46        30.35        28.96        18.25        21.90         6.51 
TCGA-56-A49D TCGA-60-2698 TCGA-60-2719 TCGA-60-2720 TCGA-63-7020 TCGA-63-A5MI 
       20.94        10.22        42.64         3.19        70.13        58.65 
TCGA-63-A5MV TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2759 TCGA-66-2763 
       36.16        43.10         2.01        21.07        25.05         0.99 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2786 TCGA-66-2789 TCGA-66-2791 TCGA-68-7755 
        2.01         3.98        25.97         4.04         5.03         2.73 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 
       12.33        29.56        23.28        11.18         0.49        73.22 
TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8139 TCGA-77-8154 TCGA-77-A5G1 
      106.95        46.78         6.51       104.09        60.53       132.36 
TCGA-77-A5G7 TCGA-85-6560 TCGA-85-7843 TCGA-85-7950 TCGA-85-8276 TCGA-85-A4CN 
        5.92        41.39         1.15        18.94        34.52        34.13 
TCGA-85-A4JB TCGA-85-A510 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4EE TCGA-92-8064 
       30.97        15.85        12.39         2.93        22.62         5.26 
TCGA-94-A4VJ TCGA-98-A53B TCGA-LA-A7SW TCGA-NC-A5HQ TCGA-O2-A52S 
       14.14         2.01        13.41        14.73        12.72 

$`11Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
      129.01       133.74         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       31.27        17.88         7.76         2.93        11.61        12.03 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 
       19.99        13.05        16.77        17.85        21.04         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 
       41.42         9.01        35.34        32.32        66.61         8.02 
TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       20.78        42.08         9.50        14.07        21.04         0.16 
TCGA-94-A5I4 TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH 
       16.14        57.07         2.76         5.69        21.21        19.10 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
        0.07        76.80        65.65        16.80         0.43         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
       75.75       117.57        11.34        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 
       92.42        86.96         2.79       154.32        49.94        46.88 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
       70.16        60.89        34.78        15.58       122.43         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 
      119.80        43.23        31.63        88.11        41.69        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       21.99         7.33         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       27.02        35.08         0.56        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       32.02        19.30         9.57        11.77        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
       44.25         0.79        86.30        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 
       18.84        30.12        62.86        16.64        97.94        79.53 
TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
      173.82        14.07        54.44        63.35         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
       36.62         6.94        44.19       118.36        27.16         2.63 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       61.61        32.88        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       50.66        16.93        44.75        39.32         4.96         1.12 
TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       38.79        33.90         4.01         0.43         0.39         7.96 
TCGA-37-4130 TCGA-37-4133 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 
        8.12         7.82        37.58        21.70       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
       68.58        55.20        82.52       102.18         1.71         1.94 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
       60.53        68.38        55.56        17.06        40.21        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 
       39.12        33.11        24.89        21.47         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       13.02         9.83         4.44        10.65        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
        0.39        29.95        28.34         5.46         8.75        27.45 
TCGA-56-5897 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
       12.43        18.48        14.53        31.27        30.41        19.76 
TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 
        0.10        17.49        33.24        14.96         4.93         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       26.89        14.07         1.35         1.81        22.75        13.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
       10.36         9.93        20.25        15.81        19.23        13.32 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.26        14.47         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 
       56.65        35.24        29.92        21.11        12.23        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       56.91        50.33        48.49        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       26.83        11.77        52.67        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
      102.67        70.62        59.97        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY 
       25.28        89.29        78.28        16.37        53.88        34.59 
TCGA-66-2727 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       16.96         0.99         1.02         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       43.99        21.01         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
        7.07        23.01        19.00         3.02        19.00        12.03 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 
       12.00        24.95         1.97        40.01        22.98        22.98 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 
       30.02        10.06        54.08         4.01        49.05         6.64 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 
        6.94        13.35        16.18        14.73        12.07        73.12 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 
       75.09       140.09        70.13         0.16        32.55        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       55.73        37.81       156.66        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       17.72        11.54        26.40        27.39         6.97        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 
       54.41        65.49        36.36       126.18       150.25        22.29 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 
       61.94        27.62        38.86         9.67        40.24         6.41 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
       36.53        34.95        31.30        32.91         1.38        29.95 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
       25.15        19.04        24.13        31.56        26.79        30.64 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       10.09         0.76        13.22        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        3.09        32.71         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC 
       38.14        12.59        18.08        22.59        30.28        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
       24.36        30.48        19.73        27.16        16.21        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED 
       15.29        29.92         3.65        24.92        11.77        20.22 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 
       10.59         2.70         3.48         4.01         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        5.03        26.63        17.69        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       27.68        21.44        30.81        30.67        21.34        27.16 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       18.15        27.02        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       16.11        13.18        11.84         4.54        64.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO 
       57.30        13.74         4.21         2.89        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q 
       25.32        26.43        83.57         3.65        33.07         3.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.13               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            151.27             173.82 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             22.49              21.47 
[1] "0.1 - 151.3 (22.5)" "0.0 - 173.8 (21.5)"
[1] "hr=" "1.2"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         0       17       23        0        14        15
  11Q GAIN WILD-TYPE       2       72      129        2        51        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  11Q GAIN MUTATED           1         13          2        3
  11Q GAIN WILD-TYPE         2         50         17        4
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 17                 72
  STAGE IB                 23                129
  STAGE II                  0                  2
  STAGE IIA                14                 51
  STAGE IIB                15                 80
  STAGE III                 1                  2
  STAGE IIIA               13                 50
  STAGE IIIB                2                 17
  STAGE IV                  3                  4
[1] 10  2
[1] 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    24  47  16   2
  11Q GAIN WILD-TYPE  88 247  55  22
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               24                 88
  T2               47                247
  T3               16                 55
  T4                2                 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                  N0  N1  N2  N3
  11Q GAIN MUTATED    55  20  10   2
  11Q GAIN WILD-TYPE 262 113  30   3
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               55                262
  N1               20                113
  N2               10                 30
  N3                2                  3
[1] 4 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    74   3
  11Q GAIN WILD-TYPE 337   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     74    3
  11Q GAIN WILD-TYPE  337    4
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               74                337
  1                3                  4
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    23  66
  11Q GAIN WILD-TYPE 107 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     23   66
  11Q GAIN WILD-TYPE  107  305
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               23                107
  MALE                 66                305
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    62  11
  11Q GAIN WILD-TYPE 322  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     62   11
  11Q GAIN WILD-TYPE  322   42
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                62                322
  YES               11                 42
[1] 2 2
[1] FALSE
D22V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED                                       2
  11Q GAIN WILD-TYPE                                    13
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  11Q GAIN MUTATED                                        1
  11Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED                                         0
  11Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                            86
  11Q GAIN WILD-TYPE                                                         393
D22V10, multiclass
                                                             clus
vv                                                            11Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               86
                                                             clus
vv                                                            11Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                393
[1] 4 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    71   3   0   6
  11Q GAIN WILD-TYPE 328   9   4  17
D22V13, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               71                328
  R1                3                  9
  R2                0                  4
  RX                6                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       2                         3    62
  11Q GAIN WILD-TYPE     7                        28   287
D22V14, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                   62                287
[1] 3 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     1  48
  11Q GAIN WILD-TYPE   7 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   48
  11Q GAIN WILD-TYPE    7  269
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               48                269
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   123  99
  12P GAIN WILD-TYPE 157 115
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               222                272 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                99                115 
$`12P GAIN MUTATED`
TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1017 TCGA-22-5471 TCGA-33-4532 
        4.80         6.18        32.19        48.82        60.66       129.01 
TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 
       19.76        28.96        31.27        11.61        12.03        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 
        3.45        17.00        16.77         0.13        41.42         9.01 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
       66.61         8.02        20.78         0.16        18.38        16.14 
TCGA-96-A4JK TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE 
       19.36        19.10         0.07        39.85        40.90         0.43 
TCGA-O2-A52W TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 
        8.58        11.34        36.07        86.96       154.32       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1079 TCGA-21-1083 TCGA-21-5782 
       46.88        99.16        34.78        31.73        43.23        31.63 
TCGA-21-5786 TCGA-21-5787 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
       33.93        10.82        14.10        20.48        35.08        48.33 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-5473 TCGA-22-5477 
       24.13        38.17        34.75        13.12        63.55        44.25 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4566 
       71.34        11.74        62.86        56.32        97.94       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASJ 
      103.53       151.27        14.07        63.35       110.99       118.36 
TCGA-34-2596 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 
        2.63        65.23        60.30        50.66        16.93        39.32 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-37-3792 TCGA-37-A5EL TCGA-39-5019 
        1.12         4.04        26.43         0.39        37.58       111.35 
TCGA-39-5021 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
       68.58        36.39        68.38        71.18        55.56        17.06 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 
       39.12        33.11        27.91        21.47         5.46        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       11.77         9.73        13.02         9.83        10.65        13.91 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
        0.39        29.95         5.46        30.35         8.75        27.45 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 
       21.90        18.48        14.53        19.76         6.51        17.49 
TCGA-56-8304 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-58-8387 TCGA-58-A46K 
        3.48        15.81        19.23        13.32        13.25        34.36 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 
       21.11        10.22        96.82        37.94        92.71        80.45 
TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
       42.64        35.90        23.57        26.83        11.77        70.13 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR 
       55.30       102.67        58.65        59.97        45.57        89.29 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2744 TCGA-66-2756 TCGA-66-2758 TCGA-66-2766 
       53.88        16.96         0.99         0.99        21.01         1.02 
TCGA-66-2767 TCGA-66-2769 TCGA-66-2777 TCGA-66-2781 TCGA-66-2785 TCGA-66-2787 
        2.01         7.07         2.01         3.98         1.97        40.01 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 
       10.06        54.08        49.05         2.73         6.64        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-7141 
       16.18        14.73        12.07        12.33        29.56         0.49 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
       73.22       106.95        46.78        32.55        55.73        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8143 TCGA-77-8148 TCGA-77-8156 
      156.66        53.92        17.72        26.40        66.51        36.36 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      132.36       150.25        22.29         5.92        61.94        27.62 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7950 TCGA-85-8048 
       41.39        36.53        34.95        32.91        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       19.04        24.13        31.56        34.52        10.09         0.76 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 
       22.45         5.29        32.71         7.76        18.08        22.59 
TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       34.13        19.73        15.85        14.96        29.92        12.39 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
        2.93        11.77        22.62        10.59         2.70         3.48 
TCGA-92-8064 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I 
        5.26        14.14        17.69        27.16         2.01        18.58 
TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG 
       20.71        16.11        13.18        11.84         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HQ TCGA-O2-A52N TCGA-O2-A52Q 
        1.22        13.74         4.21        14.73        33.07         3.72 

$`12P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 
       12.20         4.47       123.19        31.99        27.19        14.93 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 TCGA-39-5039 
       64.93        22.06       133.74         1.55        31.50        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-56-7221 
       22.49        18.38         7.76        78.18         2.93        19.99 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2715 TCGA-60-2721 TCGA-77-A5GA 
       17.85        21.04         3.58        35.34        32.32        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-96-7545 TCGA-98-8020 
       30.81         9.50        14.07        21.04        57.07         2.76 
TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 
        5.69        21.21        76.80        65.65        16.80        75.75 
TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 
      117.57        23.54        92.15        92.42         2.79        49.94 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       70.16        60.89        15.58       122.43         9.34       119.80 
TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       88.11        41.69        21.99         7.33         4.31        64.21 
TCGA-22-1011 TCGA-22-1016 TCGA-22-4596 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
        1.74        27.02         0.56        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 
       11.77        14.63         0.79        86.30        79.20        18.84 
TCGA-22-5485 TCGA-22-5492 TCGA-33-4547 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW 
       30.12        16.64        79.53        54.44         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 
       36.62         6.94        44.19        27.16        61.61        32.88 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       81.24        74.66         9.07        44.75         4.96        38.79 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       33.90         4.01         0.43         7.96         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 
        7.82         6.81         0.39         3.39        21.70       133.25 
TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
      126.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-43-2576 TCGA-43-2581 TCGA-43-6143 TCGA-43-6647 
        1.94        60.53        40.21        38.66        22.98        24.89 
TCGA-43-6773 TCGA-43-7656 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3769 
        3.81        19.59        14.20        13.32        12.16         4.44 
TCGA-51-4080 TCGA-52-7622 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7579 
        0.39        28.34        28.96        12.43        18.25        31.27 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 
       30.41         0.10        33.24        14.96         4.93        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
        9.93        20.25        20.94        18.74         0.26        14.47 
TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
        0.03        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2707 
       85.12        56.65        35.24        29.92        12.23        21.93 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 
       49.48        66.54        56.91        50.33        48.49         3.19 
TCGA-60-2722 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MM 
       29.85        52.67        70.42        68.15        70.62        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MY 
       11.34        25.28        78.28        16.37        36.16        34.59 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       43.10         2.01        21.07         1.02         2.01         0.92 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2770 
       43.99        25.05         0.99         2.01         2.01        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
       19.00         3.02        19.00        12.03        12.00        24.95 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
       25.97        22.98         4.04        22.98         5.03        30.02 
TCGA-66-2795 TCGA-68-7757 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
        4.01         6.94        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 
      140.09        70.13         0.16         6.51        86.76        12.59 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8150 
       39.09       104.09        11.54        27.39         6.97        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 
       65.49        60.53       126.18        38.86         9.67        40.24 
TCGA-85-6798 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8071 
        6.41        31.30         1.38         1.15        29.95        26.79 
TCGA-85-8072 TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 
       30.64        13.22        16.77         3.09         2.01        15.39 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC 
       36.59        38.14        12.59        30.28        30.97        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A512 TCGA-85-A5B5 
       24.36        30.48        27.16        16.21        15.29         3.65 
TCGA-90-6837 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
       24.92        20.22         4.01         2.30         4.01         5.03 
TCGA-94-8491 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       26.63        71.01        18.31        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H 
       30.81        30.67        21.34        18.15        27.02        20.32 
TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO 
       12.89        13.41        57.30         2.89        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V 
       25.32        26.43        83.57         3.65        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.07               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            173.82             140.09 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            21.685             21.815 
[1] "0.1 - 173.8 (21.7)" "0.0 - 140.1 (21.8)"
[1] "hr=" "1"  
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         2       32       65        1        31        47
  12P GAIN WILD-TYPE       0       57       87        1        34        48
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  12P GAIN MUTATED           1         33          9        2
  12P GAIN WILD-TYPE         2         30         10        5
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 32                 57
  STAGE IB                 65                 87
  STAGE II                  1                  1
  STAGE IIA                31                 34
  STAGE IIB                47                 48
  STAGE III                 1                  2
  STAGE IIIA               33                 30
  STAGE IIIB                9                 10
  STAGE IV                  2                  5
[1] 10  2
[1] 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    40 138  35  13
  12P GAIN WILD-TYPE  72 156  36  11
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               40                 72
  T2              138                156
  T3               35                 36
  T4               13                 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
  12P GAIN MUTATED   138  64  21   1
  12P GAIN WILD-TYPE 179  69  19   4
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0              138                179
  N1               64                 69
  N2               21                 19
  N3                1                  4
[1] 4 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   187   2
  12P GAIN WILD-TYPE 224   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    187    2
  12P GAIN WILD-TYPE  224    5
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0              187                224
  1                2                  5
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    44 182
  12P GAIN WILD-TYPE  86 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     44  182
  12P GAIN WILD-TYPE   86  189
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               44                 86
  MALE                182                189
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   173  26
  12P GAIN WILD-TYPE 211  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    173   26
  12P GAIN WILD-TYPE  211   27
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO               173                211
  YES               26                 27
[1] 2 2
[1] FALSE
D23V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                       7
  12P GAIN WILD-TYPE                                     8
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  12P GAIN MUTATED                                        2
  12P GAIN WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                         0
  12P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                           217
  12P GAIN WILD-TYPE                                                         262
D23V10, multiclass
                                                             clus
vv                                                            12P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              217
                                                             clus
vv                                                            12P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D23V11, continuous
D23V12, continuous
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED   177   5   2  12
  12P GAIN WILD-TYPE 222   7   2  11
D23V13, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0              177                222
  R1                5                  7
  R2                2                  2
  RX               12                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       4                        16   164
  12P GAIN WILD-TYPE     5                        15   185
D23V14, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN               16                 15
  WHITE                                  164                185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     4 145
  12P GAIN WILD-TYPE   4 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4  145
  12P GAIN WILD-TYPE    4  172
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              145                172
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    81  68
  12Q GAIN WILD-TYPE 199 146
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               149                345 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                68                146 
$`12Q GAIN MUTATED`
TCGA-18-3410 TCGA-18-4083 TCGA-22-1017 TCGA-22-5471 TCGA-33-4532 TCGA-33-6737 
        4.80         6.18        48.82        60.66       129.01        19.76 
TCGA-34-2605 TCGA-34-2609 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-A5DR 
       28.96        31.27        13.05         3.45        17.00         0.13 
TCGA-60-2712 TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-94-7557 
        9.01        35.34        66.61         8.02        20.78         0.16 
TCGA-94-7943 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE 
       18.38        19.10         0.07        39.85        40.90         0.43 
TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 
       11.34        36.07        86.96       154.32       119.54        46.88 
TCGA-21-1072 TCGA-21-1077 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-1016 
       99.16        34.78        43.23        33.93        10.82        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 TCGA-22-5473 
       20.48        35.08        48.33        34.75        13.12        63.55 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5491 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 
       71.34        11.74        56.32        97.94       103.53       151.27 
TCGA-33-4586 TCGA-34-2596 TCGA-34-5231 TCGA-34-5239 TCGA-34-7107 TCGA-34-8455 
       14.07         2.63        65.23        60.30         1.12         4.04 
TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5019 
        0.39         8.12         3.39        37.58       133.25       111.35 
TCGA-39-5035 TCGA-43-3394 TCGA-43-3920 TCGA-43-6771 TCGA-43-8116 TCGA-43-A475 
       68.38        39.12        33.11         5.46        11.77         9.73 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-52-7809 TCGA-52-7812 TCGA-56-7582 
        9.83        10.65         0.39         5.46        27.45        19.76 
TCGA-56-7822 TCGA-56-8304 TCGA-56-A4BX TCGA-58-A46K TCGA-60-2695 TCGA-60-2698 
       17.49         3.48        13.32        34.36        21.11        10.22 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2719 TCGA-60-2724 TCGA-60-2725 
       37.94        92.71        80.45        42.64        23.57        26.83 
TCGA-60-2726 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR 
       11.77        55.30       102.67        59.97        45.57        89.29 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2766 TCGA-66-2767 TCGA-66-2781 TCGA-66-2787 
        2.01         0.99         1.02         2.01         3.98        40.01 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 
       10.06        54.08        49.05         2.73         6.64        13.35 
TCGA-70-6723 TCGA-77-6842 TCGA-77-7142 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
       12.33        29.56        73.22        32.55        55.73        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 
      156.66        53.92        26.40        66.51        54.41        60.53 
TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 
      150.25         5.92        27.62        18.94        24.13        31.56 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8353 TCGA-85-8354 TCGA-85-8664 
       34.52        10.09        22.45         3.09        32.71        18.08 
TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A510 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-7767 
       34.13        19.73        15.85        29.92         3.65         2.93 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-98-8023 
       11.77        22.62        10.59         2.70         3.48        21.34 
TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HF 
       27.16         2.01        18.58        16.11        13.18         4.54 
TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HQ TCGA-O2-A52Q 
       64.54        13.74         4.21        14.73         3.72 

$`12Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI 
       12.20         4.47       123.19        31.99        27.19        32.19 
TCGA-22-1000 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 
       14.93        64.93        22.06       133.74         1.55        31.50 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       17.88        22.49        18.38         7.76        78.18         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ 
       11.61        12.03        19.99        16.77        17.85        21.04 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2721 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 
        3.58        41.42        32.32        42.08        30.81         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
       14.07        21.04        16.14        57.07        19.36         2.76 
TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W 
        5.69        21.21        76.80        65.65        16.80         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 
       75.75       117.57        23.54        92.15        92.42         2.79 
TCGA-18-5592 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       49.94        70.16        60.89        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 
        9.34       119.80        31.63        88.11        41.69        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4595 
        7.33         4.31        64.21         1.74        14.10        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
        0.56        38.17        32.02        19.30         9.57        11.77 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 
       14.63        44.25         0.79        86.30        79.20        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 
       30.12        62.86        16.64        79.53       173.82        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       63.35         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 
       44.19       118.36        27.16        61.61        32.88        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       74.66         9.07        50.66        16.93        44.75        39.32 
TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        4.96        38.79        26.43        33.90         4.01         0.43 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EN 
        7.96         7.46         7.82         6.81         0.39        21.70 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      126.58        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 
       24.33         1.94        60.53        36.39        71.18        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       17.06        40.21        38.66        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-A56U TCGA-46-3765 
       21.47         3.81        19.59        13.38        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 
       12.16        13.02         4.44        13.91         0.39        29.95 
TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       28.34        30.35         8.75        28.96        12.43        18.25 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 
       21.90        18.48        14.53        31.27        30.41         6.51 
TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 
        0.10        33.24        14.96         4.93        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS 
       20.25        15.81        20.94        19.23        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
       14.47         0.03        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       16.47        34.78        85.12        56.65        35.24        29.92 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       12.23        96.82        21.93        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-63-6202 
       50.33        48.49         3.19        29.85        35.90        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM 
       70.13        70.42        68.15        70.62        58.65        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       11.34        25.28        78.28        16.37        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       34.59        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        1.02         0.92        43.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
        2.01         2.01         7.07        23.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
        2.01        19.00        12.03        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
       25.97        22.98         4.04        22.98         5.03        30.02 
TCGA-66-2795 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 
        4.01         6.94        16.18        14.73        12.07        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 
       75.09        23.28        11.18       140.09         0.49        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 
      106.95         0.16        46.78         6.51        86.76        12.59 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
       39.09        17.72       104.09        11.54        27.39         6.97 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G8 
       65.49        36.36       126.18       132.36        22.29        61.94 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       38.86         9.67        41.39        40.24         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       34.95        31.30        32.91         1.38         1.15        29.95 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 
       25.15        19.04        26.79        30.64         0.76        13.22 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
       16.77         5.29         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC 
       38.14        12.59        22.59        30.28        30.97        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
       24.36        30.48        27.16        16.21        14.96        15.29 
TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       12.39        24.92        20.22         4.01         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        26.63        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       18.31        17.46        27.68        21.44        30.81        30.67 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A7SW 
       18.15        27.02        20.32        20.71        12.89        13.41 
TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO 
       11.84         1.22        57.30         2.89        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52S 
       25.32        26.43        83.57         3.65        33.07        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            156.66             173.82 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             22.45              21.70 
[1] "0.1 - 156.7 (22.4)" "0.0 - 173.8 (21.7)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0       26       36        1        18        32
  12Q GAIN WILD-TYPE       2       63      116        1        47        63
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  12Q GAIN MUTATED           1         25          8        2
  12Q GAIN WILD-TYPE         2         38         11        5
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 26                 63
  STAGE IB                 36                116
  STAGE II                  1                  1
  STAGE IIA                18                 47
  STAGE IIB                32                 63
  STAGE III                 1                  2
  STAGE IIIA               25                 38
  STAGE IIIB                8                 11
  STAGE IV                  2                  5
[1] 10  2
[1] 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    31  84  25  11
  12Q GAIN WILD-TYPE  81 210  46  13
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               31                 81
  T2               84                210
  T3               25                 46
  T4               11                 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
  12Q GAIN MUTATED    85  46  17   1
  12Q GAIN WILD-TYPE 232  87  23   4
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               85                232
  N1               46                 87
  N2               17                 23
  N3                1                  4
[1] 4 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   128   2
  12Q GAIN WILD-TYPE 283   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    128    2
  12Q GAIN WILD-TYPE  283    5
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0              128                283
  1                2                  5
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    26 125
  12Q GAIN WILD-TYPE 104 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     26  125
  12Q GAIN WILD-TYPE  104  246
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               26                104
  MALE                125                246
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   112  20
  12Q GAIN WILD-TYPE 272  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    112   20
  12Q GAIN WILD-TYPE  272   33
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO               112                272
  YES               20                 33
[1] 2 2
[1] FALSE
D24V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                       5
  12Q GAIN WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  12Q GAIN MUTATED                                        1
  12Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                         0
  12Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                           145
  12Q GAIN WILD-TYPE                                                         334
D24V10, multiclass
                                                             clus
vv                                                            12Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              145
                                                             clus
vv                                                            12Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D24V11, continuous
D24V12, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED   124   3   1   6
  12Q GAIN WILD-TYPE 275   9   3  17
D24V13, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0              124                275
  R1                3                  9
  R2                1                  3
  RX                6                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         9   110
  12Q GAIN WILD-TYPE     7                        22   239
D24V14, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                9                 22
  WHITE                                  110                239
[1] 3 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     3  95
  12Q GAIN WILD-TYPE   5 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   95
  12Q GAIN WILD-TYPE    5  222
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               95                222
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    21  18
  13Q GAIN WILD-TYPE 259 196
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                39                455 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                18                196 
$`13Q GAIN MUTATED`
TCGA-18-3407 TCGA-33-4533 TCGA-43-7657 TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 
        4.47       133.74         7.76        12.03        13.05         3.45 
TCGA-94-7943 TCGA-18-3412 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-22-4599 
       18.38        11.34        31.73         9.34       119.80        38.17 
TCGA-33-AASB TCGA-34-8455 TCGA-34-A5IX TCGA-37-4130 TCGA-37-A5EL TCGA-37-A5EN 
        6.94         4.04        33.90         8.12        37.58        21.70 
TCGA-39-5034 TCGA-39-5035 TCGA-43-2576 TCGA-51-4081 TCGA-52-7810 TCGA-56-5897 
       36.39        68.38        40.21        29.95        30.35        12.43 
TCGA-56-5898 TCGA-56-7223 TCGA-56-7822 TCGA-56-A4BX TCGA-60-2698 TCGA-63-A5MT 
       18.25        14.53        17.49        13.32        10.22        16.37 
TCGA-66-2737 TCGA-66-2791 TCGA-70-6723 TCGA-85-7696 TCGA-85-7843 TCGA-85-A4JC 
        2.01         5.03        12.33        36.53         1.15        19.86 
TCGA-85-A50M TCGA-90-A59Q TCGA-MF-A522 
       27.16        10.59        11.84 

$`13Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20       123.19         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      129.01         1.55        19.76        31.50        28.96        31.27 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
       17.88        22.49        18.38        78.18         2.93        11.61 
TCGA-56-7221 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
       19.99        17.00        16.77        17.85        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
        3.58        41.42         9.01        35.34        32.32        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
        8.02        20.78        42.08        30.81         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
       21.04         0.16        16.14        57.07        19.36         2.76 
TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        5.69        21.21        19.10         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       40.90        65.65        16.80         0.43         8.58        75.75 
TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
      117.57        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2.79       154.32        49.94       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 
       70.16        60.89        34.78        15.58       122.43        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
       31.63        88.11        41.69        33.93        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        7.33         4.31        64.21         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
       20.48        35.08        48.33        24.13         0.56        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       13.12        32.02        19.30         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       14.63        44.25         0.79        86.30        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       11.74        18.84        30.12        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       97.94        79.53       173.82       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD 
       54.44        63.35         4.70         0.30        36.62       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
       44.19       118.36        27.16         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        81.24        74.66         9.07        60.30        50.66 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        44.75        39.32         4.96         1.12        38.79 
TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
       26.43         4.01         0.43         0.39         7.96         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
        7.82         6.81         0.39         3.39       133.25       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      111.35        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
       24.33         1.94        60.53        71.18        55.56        17.06 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       38.66        39.12        33.11        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       21.47         5.46         3.81        19.59        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
        9.73        14.20        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
        4.44        10.65        13.91         0.39         0.39        28.34 
TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-7222 
        5.46         8.75        27.45        28.96        21.90        18.48 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 
       31.27        30.41        19.76         6.51         0.10        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       14.96         4.93         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75        13.81        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       15.81        20.94        19.23        18.74         0.26        14.47 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.03        13.25        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       34.78        85.12        34.36        56.65        35.24        29.92 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       21.11        12.23        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       80.45        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW 
       11.34        25.28        89.29        78.28        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       34.59        16.96        43.10        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        2.01         0.92         0.99        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
        0.99         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
       23.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        3.98        12.00        24.95         1.97        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
       22.98         4.04        22.98        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
        4.01        49.05         2.73         6.64         6.94        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       16.18        14.73        12.07        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       23.28        11.18       140.09         0.49        73.22        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
      106.95         0.16        46.78        32.55         6.51        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       55.73        37.81       156.66        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       17.72       104.09        11.54        26.40        27.39         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       66.51        54.41        65.49        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      132.36       150.25        22.29         5.92        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 
       38.86         9.67        41.39        40.24         6.41        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       31.30        32.91         1.38        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       19.04        24.13        31.56        26.79        30.64        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       10.09         0.76        13.22        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        3.09        32.71         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       38.14        12.59        18.08        22.59        30.28        34.13 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
       30.97        24.36        30.48        19.73        16.21        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       14.96        15.29        29.92        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 
        2.93        11.77        20.22        22.62         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         5.26         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       14.14        17.69        71.01        18.31        17.46        27.68 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A 
       21.44        30.81        30.67        21.34        27.16        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
        2.01        27.02        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       16.11        13.18        13.41         4.54        64.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO 
       57.30        13.74         4.21         2.89        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       25.32        14.73        26.43        83.57         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        12.72        43.89        11.18         0.20 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              1.15               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            133.74             173.82 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             14.53              22.49 
[1] "1.1 - 133.7 (14.5)" "0.0 - 173.8 (22.5)"
[1] "hr=" "1.4"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         0        7        8        0         6        11
  13Q GAIN WILD-TYPE       2       82      144        2        59        84
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  13Q GAIN MUTATED           0          4          2        1
  13Q GAIN WILD-TYPE         3         59         17        6
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  7                 82
  STAGE IB                  8                144
  STAGE II                  0                  2
  STAGE IIA                 6                 59
  STAGE IIB                11                 84
  STAGE III                 0                  3
  STAGE IIIA                4                 59
  STAGE IIIB                2                 17
  STAGE IV                  1                  6
[1] 10  2
[1] 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     7  21   9   2
  13Q GAIN WILD-TYPE 105 273  62  22
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                7                105
  T2               21                273
  T3                9                 62
  T4                2                 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                  N0  N1  N2  N3
  13Q GAIN MUTATED    26   8   3   1
  13Q GAIN WILD-TYPE 291 125  37   4
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               26                291
  N1                8                125
  N2                3                 37
  N3                1                  4
[1] 4 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    29   1
  13Q GAIN WILD-TYPE 382   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     29    1
  13Q GAIN WILD-TYPE  382    6
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               29                382
  1                1                  6
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     8  31
  13Q GAIN WILD-TYPE 122 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      8   31
  13Q GAIN WILD-TYPE  122  340
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                8                122
  MALE                 31                340
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    26   6
  13Q GAIN WILD-TYPE 358  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     26    6
  13Q GAIN WILD-TYPE  358   47
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                26                358
  YES                6                 47
[1] 2 2
[1] FALSE
D25V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED                                       0
  13Q GAIN WILD-TYPE                                    15
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  13Q GAIN MUTATED                                        1
  13Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED                                         0
  13Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                            38
  13Q GAIN WILD-TYPE                                                         441
D25V10, multiclass
                                                             clus
vv                                                            13Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               38
                                                             clus
vv                                                            13Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       15
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                441
[1] 4 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    28   1   0   2
  13Q GAIN WILD-TYPE 371  11   4  21
D25V13, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               28                371
  R1                1                 11
  R2                0                  4
  RX                2                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       3                         4    29
  13Q GAIN WILD-TYPE     6                        27   320
D25V14, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                4                 27
  WHITE                                   29                320
[1] 3 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     0  33
  13Q GAIN WILD-TYPE   8 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   33
  13Q GAIN WILD-TYPE    8  284
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               33                284
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    76  47
  14Q GAIN WILD-TYPE 204 167
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               123                371 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                47                167 
$`14Q GAIN MUTATED`
TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 
       60.66        22.06       129.01       133.74         1.55        19.76 
TCGA-43-2578 TCGA-43-8118 TCGA-43-A56V TCGA-56-8504 TCGA-96-A4JK TCGA-98-8020 
       22.49         2.93        12.03        16.77        19.36         2.76 
TCGA-98-A539 TCGA-NC-A5HM TCGA-NC-A5HR TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
        5.69        39.85        40.90         8.58        75.75       117.57 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3421 TCGA-18-5592 TCGA-21-1076 TCGA-21-1079 
       11.34        92.15        86.96        49.94        60.89        31.73 
TCGA-21-1082 TCGA-21-5786 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-33-4566 
      119.80        33.93        20.48        35.08        24.13       173.82 
TCGA-33-4582 TCGA-33-AASD TCGA-33-AASI TCGA-34-8455 TCGA-34-8456 TCGA-37-3792 
      103.53       110.99        44.19         4.04        26.43         0.39 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 TCGA-43-6143 
        3.39       133.25        24.33        60.53        55.56        22.98 
TCGA-43-6771 TCGA-46-6025 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-56-1622 
        5.46        10.65        29.95        28.34         8.75        28.96 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7580 TCGA-56-7730 TCGA-56-7823 TCGA-56-8304 
       18.25        21.90        30.41         6.51        33.24         3.48 
TCGA-56-8624 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8393 
       13.81        15.81        20.94        18.74        14.47        34.78 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       35.24        29.92        10.22        92.71        21.93        80.45 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2724 TCGA-63-7020 TCGA-63-7022 TCGA-63-A5MG 
       42.64        29.85        23.57        70.13        68.15        70.62 
TCGA-63-A5MI TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2771 
       58.65         0.99         0.99         0.99         2.01        19.00 
TCGA-66-2782 TCGA-66-2788 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 
       12.00        22.98        30.02        10.06        49.05         2.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-7138 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 
       12.07        12.33        11.18        73.22       106.95        46.78 
TCGA-77-8007 TCGA-77-8130 TCGA-77-8136 TCGA-77-8139 TCGA-77-8143 TCGA-77-8150 
        6.51       156.66        39.09       104.09        26.40        54.41 
TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6175 TCGA-85-6561 
       65.49       150.25        22.29        61.94         9.67        40.24 
TCGA-85-7698 TCGA-85-8353 TCGA-85-8355 TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A50M 
       31.30         3.09         2.01        30.97        30.48        27.16 
TCGA-85-A5B5 TCGA-92-7340 TCGA-92-7341 TCGA-98-A538 TCGA-L3-A4E7 TCGA-L3-A524 
        3.65         2.70         3.48        27.16        12.89        16.11 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX 
       64.54        57.30        25.32        14.73        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V 
       33.07         3.72        43.89 

$`14Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-34-2604 
       27.19        32.19        14.93        48.82        64.93        31.50 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       28.96        31.27        17.88        18.38         7.76        78.18 
TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY 
       11.61        19.99        13.05         3.45        17.00        17.85 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       21.04         0.13         3.58        41.42         9.01        35.34 
TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       32.32        66.61         8.02        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        9.50        14.07        21.04         0.16        18.38        16.14 
TCGA-96-7545 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A5CT 
       57.07        21.21        19.10         0.07        76.80        65.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 
       16.80         0.43        23.54        36.07        92.42         2.79 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 
      154.32       119.54        46.88        99.16        70.16        34.78 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       15.58       122.43         9.34        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       41.69        10.82        21.99         7.33         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
        1.74        14.10        27.02        48.33         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       34.75        13.12        32.02        19.30         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       63.55        14.63        44.25         0.79        86.30        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       16.64        97.94        79.53       151.27        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ 
       63.35         4.70         0.30        36.62         6.94       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
       39.32         4.96         1.12        38.79        33.90         4.01 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         7.96         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        0.39        37.58        21.70       126.58       111.35        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 
       55.20        82.52       102.18         1.71         1.94        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       68.38        71.18        17.06        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 
       33.11        27.91        24.89        21.47         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       13.02         9.83         4.44        13.91         0.39         0.39 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-7222 TCGA-56-7223 
        5.46        30.35        27.45        12.43        18.48        14.53 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 
       31.27        19.76         0.10        17.49        14.96         4.93 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 
       26.89        14.07         1.35         1.81        22.75        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8386 
        9.93        20.25        19.23        13.32         0.26         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J 
       13.25        13.55        29.95        71.24        16.47        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       34.36        56.65        21.11        12.23        96.82        37.94 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 
       49.48        66.54        56.91        50.33        48.49         3.19 
TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 
       35.90        26.83        11.77        52.67        70.42        55.30 
TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
      102.67        59.97        45.57        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       89.29        78.28        16.37        36.16        53.88        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 
       16.96        43.10         2.01        21.07         1.02         2.01 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 
        0.92        43.99        21.01        25.05         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01         7.07        23.01         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
       12.03         3.98        24.95         1.97        25.97        40.01 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7756 
        4.04        22.98         5.03        54.08         4.01         6.64 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
        6.94        13.35        16.18        14.73        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7338 
       75.09        23.28       140.09         0.49        70.13         0.16 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
       32.55        86.76        55.73        37.81        12.59        53.92 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 
       17.72        11.54        27.39         6.97        66.51        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH 
       36.36       126.18       132.36         5.92        27.62        38.86 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
       41.39         6.41        36.53        34.95        32.91         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1.15        29.95        18.94        25.15        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       31.56        26.79        30.64        34.52        10.09         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 
       13.22        22.45        16.77         5.29        32.71        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        7.76        36.59        38.14        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z 
       30.28        34.13        19.86        24.36        19.73        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       15.85        14.96        15.29        29.92        12.39        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 
        2.93        11.77        20.22        22.62        10.59         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        5.26         2.30         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       17.69        71.01        18.31        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.81        30.67        21.34        18.15         2.01        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.32        18.58        20.71        13.18        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
        4.54         1.22        13.74         4.21         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HT TCGA-O2-A52S TCGA-O2-A5IB TCGA-XC-AA0X 
       43.92        26.43        12.72        11.18         0.20 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.39               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            173.82             154.32 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             26.43              20.32 
[1] "0.4 - 173.8 (26.4)" "0.0 - 154.3 (20.3)"
[1] "hr=" "1.5"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         2       15       40        1        16        27
  14Q GAIN WILD-TYPE       0       74      112        1        49        68
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  14Q GAIN MUTATED           1         19          3        2
  14Q GAIN WILD-TYPE         2         44         16        5
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 15                 74
  STAGE IB                 40                112
  STAGE II                  1                  1
  STAGE IIA                16                 49
  STAGE IIB                27                 68
  STAGE III                 1                  2
  STAGE IIIA               19                 44
  STAGE IIIB                3                 16
  STAGE IV                  2                  5
[1] 10  2
[1] 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    20  81  21   4
  14Q GAIN WILD-TYPE  92 213  50  20
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               20                 92
  T2               81                213
  T3               21                 50
  T4                4                 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                  N0  N1  N2  N3
  14Q GAIN MUTATED    81  30  14   0
  14Q GAIN WILD-TYPE 236 103  26   5
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               81                236
  N1               30                103
  N2               14                 26
  N3                0                  5
[1] 4 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   104   2
  14Q GAIN WILD-TYPE 307   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    104    2
  14Q GAIN WILD-TYPE  307    5
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0              104                307
  1                2                  5
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    34  92
  14Q GAIN WILD-TYPE  96 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     34   92
  14Q GAIN WILD-TYPE   96  279
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               34                 96
  MALE                 92                279
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED   100  15
  14Q GAIN WILD-TYPE 284  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    100   15
  14Q GAIN WILD-TYPE  284   38
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO               100                284
  YES               15                 38
[1] 2 2
[1] FALSE
D26V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                       4
  14Q GAIN WILD-TYPE                                    11
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  14Q GAIN MUTATED                                        1
  14Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                         0
  14Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                           121
  14Q GAIN WILD-TYPE                                                         358
D26V10, multiclass
                                                             clus
vv                                                            14Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              121
                                                             clus
vv                                                            14Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
D26V12, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    99   4   1   8
  14Q GAIN WILD-TYPE 300   8   3  15
D26V13, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               99                300
  R1                4                  8
  R2                1                  3
  RX                8                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       3                         9    82
  14Q GAIN WILD-TYPE     6                        22   267
D26V14, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                9                 22
  WHITE                                   82                267
[1] 3 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     5  72
  14Q GAIN WILD-TYPE   3 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   72
  14Q GAIN WILD-TYPE    3  245
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  3
  NOT HISPANIC OR LATINO               72                245
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    60  46
  15Q GAIN WILD-TYPE 220 168
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               106                388 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                46                168 
$`15Q GAIN MUTATED`
TCGA-18-3410 TCGA-18-4083 TCGA-22-5472 TCGA-34-2605 TCGA-34-2609 TCGA-56-8308 
        4.80         6.18        64.93        28.96        31.27        17.00 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-77-7140 TCGA-94-7943 TCGA-94-A5I4 
        0.13         3.58        41.42        20.78        18.38        16.14 
TCGA-96-7545 TCGA-98-8020 TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3414 
       57.07         2.76        76.80        40.90         0.43        23.54 
TCGA-18-3417 TCGA-18-3421 TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 TCGA-21-5786 
       36.07        86.96        34.78        31.73       119.80        33.93 
TCGA-22-4593 TCGA-22-4604 TCGA-22-4605 TCGA-22-5474 TCGA-22-5482 TCGA-22-5483 
       35.08        13.12        32.02        14.63        11.74        18.84 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-34-2596 TCGA-34-5231 TCGA-34-5240 
       97.94       173.82       151.27         2.63        65.23        50.66 
TCGA-34-8455 TCGA-37-3792 TCGA-37-A5EN TCGA-39-5037 TCGA-43-3394 TCGA-43-6770 
        4.04         0.39        21.70        55.56        39.12        21.47 
TCGA-43-A475 TCGA-52-7809 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-8082 
        9.73         5.46        18.48        31.27        19.76        14.96 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46K TCGA-60-2695 TCGA-60-2706 TCGA-60-2710 
       71.24        34.78        34.36        21.11        92.71        66.54 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-63-7020 TCGA-63-A5MI 
       42.64        29.85        23.57        26.83        70.13        58.65 
TCGA-63-A5MP TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2734 TCGA-66-2754 TCGA-66-2767 
       25.28        36.16        34.59        43.10         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-68-7755 TCGA-77-7141 
        7.07        23.01        19.00         3.02         2.73         0.49 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8133 TCGA-77-8136 TCGA-77-8150 TCGA-77-A5G1 
       46.78        32.55        53.92        39.09        54.41       132.36 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7844 TCGA-85-7950 
       27.62        40.24         6.41        36.53        29.95        18.94 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8351 
       19.04        24.13        31.56        34.52        10.09        16.77 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8481 TCGA-85-8664 TCGA-85-A4CN TCGA-85-A4JC 
        5.29        32.71         7.76        18.08        34.13        19.86 
TCGA-85-A50Z TCGA-85-A510 TCGA-90-7769 TCGA-90-A59Q TCGA-92-7341 TCGA-94-A5I6 
       16.21        15.85        11.77        10.59         3.48        17.69 
TCGA-98-A538 TCGA-98-A53B TCGA-L3-A524 TCGA-LA-A446 
       27.16         2.01        16.11        13.18 

$`15Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI 
       12.20         4.47       123.19        31.99        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       14.93        48.82        60.66        22.06       129.01       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 
        1.55        19.76        31.50        17.88        22.49        18.38 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
        7.76        78.18         2.93        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2712 
       13.05         3.45        16.77        17.85        21.04         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32        66.61         8.02        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-96-A4JK TCGA-98-A539 
        9.50        14.07        21.04         0.16        19.36         5.69 
TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 
       21.21        19.10         0.07        39.85        65.65        16.80 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3419 
        8.58        75.75       117.57        11.34        92.15        92.42 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2.79       154.32        49.94       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
       70.16        60.89        15.58       122.43         9.34        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
       31.63        88.11        41.69        10.82        21.99         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
        4.31        64.21         1.74        14.10        27.02        20.48 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 
       48.33        24.13         0.56        38.17        34.75        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
        9.57        11.77        63.55        44.25         0.79        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       71.34        79.20        30.12        62.86        56.32        16.64 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
       79.53       103.53        14.07        54.44        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        0.30        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       27.16        61.61        32.88        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       60.30        16.93        44.75        39.32         4.96         1.12 
TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
       38.79        26.43        33.90         4.01         0.43         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        8.12         7.46         7.82         6.81         0.39         3.39 
TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
       37.58       133.25       126.58       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
       36.39        68.38        71.18        17.06        40.21        38.66 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 
       33.11        27.91        22.98        24.89         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       19.59        13.38        11.77        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       13.02         9.83         4.44        10.65        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
        0.39        29.95        28.34        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7580 
       28.96        12.43        18.25        21.90        14.53        30.41 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 
        6.51         0.10        17.49        33.24         4.93         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       26.89        14.07         1.35         1.81        22.75        13.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
       10.36         9.93        20.25        15.81        20.94        19.23 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       13.32        18.74         0.26        14.47         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
       13.55        29.95        16.47        85.12        56.65        35.24 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 
       29.92        12.23        10.22        96.82        37.94        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 
       80.45        49.48        56.91        50.33        48.49         3.19 
TCGA-60-2723 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       35.90        11.77        52.67        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
      102.67        70.62        59.97        45.57        14.99        11.34 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2727 TCGA-66-2737 
       89.29        78.28        16.37        53.88        16.96         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
       21.07         0.99         1.02         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        2.01        19.00        12.03         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1.97        25.97        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        6.64         6.94        13.35        16.18        14.73        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.33        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 
      140.09        73.22        70.13       106.95         0.16         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 
       86.76        55.73        37.81       156.66        12.59        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
      104.09        11.54        26.40        27.39         6.97        66.51 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 
       65.49        60.53        36.36       126.18       150.25        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 
        5.92        61.94        38.86         9.67        41.39        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8071 
       31.30        32.91         1.38         1.15        25.15        26.79 
TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8353 TCGA-85-8355 
       30.64         0.76        13.22        22.45         3.09         2.01 
TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL 
       15.39        36.59        38.14        12.59        22.59        30.28 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A511 
       30.97        24.36        30.48        19.73        27.16        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 
       15.29        29.92        12.39         3.65        24.92         2.93 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       20.22        22.62         2.70         4.01         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        4.01         5.03        26.63        14.14        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44        30.81        30.67        21.34 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       18.15        27.02        20.32        18.58        20.71        12.89 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       13.41        11.84         4.54        64.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21         2.89        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q 
       14.73        26.43        83.57         3.65        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89        11.18         0.20 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.13               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            173.82             156.66 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             23.85              21.14 
[1] "0.1 - 173.8 (23.9)" "0.0 - 156.7 (21.1)"
[1] "hr=" "1"  
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         0       10       33        0        19        23
  15Q GAIN WILD-TYPE       2       79      119        2        46        72
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  15Q GAIN MUTATED           0         14          5        3
  15Q GAIN WILD-TYPE         3         49         14        4
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 10                 79
  STAGE IB                 33                119
  STAGE II                  0                  2
  STAGE IIA                19                 46
  STAGE IIB                23                 72
  STAGE III                 0                  3
  STAGE IIIA               14                 49
  STAGE IIIB                5                 14
  STAGE IV                  3                  4
[1] 10  2
[1] 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    17  68  16   6
  15Q GAIN WILD-TYPE  95 226  55  18
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               17                 95
  T2               68                226
  T3               16                 55
  T4                6                 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
  15Q GAIN MUTATED    58  38   8   1
  15Q GAIN WILD-TYPE 259  95  32   4
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               58                259
  N1               38                 95
  N2                8                 32
  N3                1                  4
[1] 4 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    93   3
  15Q GAIN WILD-TYPE 318   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     93    3
  15Q GAIN WILD-TYPE  318    4
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               93                318
  1                3                  4
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    22  85
  15Q GAIN WILD-TYPE 108 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     22   85
  15Q GAIN WILD-TYPE  108  286
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               22                108
  MALE                 85                286
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    87  11
  15Q GAIN WILD-TYPE 297  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     87   11
  15Q GAIN WILD-TYPE  297   42
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                87                297
  YES               11                 42
[1] 2 2
[1] FALSE
D27V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                       5
  15Q GAIN WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  15Q GAIN MUTATED                                        1
  15Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                         0
  15Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                           101
  15Q GAIN WILD-TYPE                                                         378
D27V10, multiclass
                                                             clus
vv                                                            15Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              101
                                                             clus
vv                                                            15Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                378
[1] 4 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    89   3   0   6
  15Q GAIN WILD-TYPE 310   9   4  17
D27V13, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               89                310
  R1                3                  9
  R2                0                  4
  RX                6                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         6    79
  15Q GAIN WILD-TYPE     8                        25   270
D27V14, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                6                 25
  WHITE                                   79                270
[1] 3 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     1  74
  15Q GAIN WILD-TYPE   7 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   74
  15Q GAIN WILD-TYPE    7  243
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               74                243
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    47  38
  16P GAIN WILD-TYPE 233 176
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                85                409 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                176 
$`16P GAIN MUTATED`
TCGA-18-5595 TCGA-22-1017 TCGA-33-4532 TCGA-34-2604 TCGA-43-2578 TCGA-43-5668 
       27.19        48.82       129.01        31.50        22.49        18.38 
TCGA-43-A56V TCGA-56-8305 TCGA-56-8504 TCGA-77-A5GA TCGA-94-A5I4 TCGA-98-8020 
       12.03         3.45        16.77        42.08        16.14         2.76 
TCGA-J1-A4AH TCGA-NC-A5HM TCGA-18-3412 TCGA-21-1071 TCGA-21-1072 TCGA-21-1081 
       19.10        39.85        11.34        46.88        99.16         9.34 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5787 TCGA-22-1011 TCGA-22-4593 TCGA-33-4566 
       43.23        88.11        10.82         1.74        35.08       173.82 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-34-5240 TCGA-34-5241 TCGA-34-7107 
      151.27        14.07        54.44        50.66        16.93         1.12 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
       26.43        33.90         6.81         0.39         3.39        37.58 
TCGA-37-A5EN TCGA-39-5034 TCGA-39-5036 TCGA-43-2576 TCGA-52-7811 TCGA-56-1622 
       21.70        36.39        71.18        40.21         8.75        28.96 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-8304 TCGA-56-A4BW TCGA-58-8386 
       21.90        18.48        14.53         3.48        19.23         0.03 
TCGA-60-2706 TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-A5MV 
       92.71        29.85        26.83        11.77        70.13        36.16 
TCGA-66-2737 TCGA-66-2756 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2791 
        2.01         0.99         2.01         2.01        23.01         5.03 
TCGA-66-2793 TCGA-70-6722 TCGA-70-6723 TCGA-77-7465 TCGA-77-8009 TCGA-77-8139 
       10.06        12.07        12.33        32.55        55.73       104.09 
TCGA-77-8150 TCGA-77-A5G1 TCGA-85-6175 TCGA-85-6560 TCGA-85-7843 TCGA-85-8072 
       54.41       132.36         9.67        41.39         1.15        30.64 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 TCGA-85-A4JB TCGA-85-A510 TCGA-90-A59Q 
       34.52         0.76        22.45        30.97        15.85        10.59 
TCGA-92-7341 TCGA-94-A4VJ TCGA-98-8022 TCGA-98-A53J TCGA-NC-A5HO TCGA-NC-A5HQ 
        3.48        14.14        30.67        20.71        43.92        14.73 
TCGA-NK-A5CX 
        3.65 

$`16P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 
       32.19        14.93        60.66        64.93        22.06       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-7657 
        1.55        19.76        28.96        31.27        17.88         7.76 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 
       78.18         2.93        11.61        19.99        13.05        17.00 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
       17.85        21.04         0.13         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB 
       35.34        32.32        66.61         8.02        20.78        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7545 
        9.50        14.07        21.04         0.16        18.38        57.07 
TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HR 
       19.36         5.69        21.21         0.07        76.80        40.90 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       65.65        16.80         0.43         8.58        75.75       117.57 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       23.54        92.15        36.07        92.42        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      154.32        49.94       119.54        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 
       15.58        31.73       122.43       119.80        31.63        41.69 
TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 
       33.93        21.99         7.33         4.31        64.21        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       27.02        20.48        48.33        24.13         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       34.75        13.12        32.02        19.30         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       63.55        14.63        44.25         0.79        86.30        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-6738 TCGA-33-A4WN 
       16.64        97.94        79.53       103.53        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        0.30        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       74.66         9.07        60.30        44.75        39.32         4.96 
TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       38.79         4.04         4.01         0.43         0.39         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        8.12         7.46         7.82       133.25       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 
        1.94        60.53        68.38        55.56        17.06        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       39.12        33.11        27.91        22.98        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
        5.46         3.81        19.59        13.38        11.77         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       14.20        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       10.65        13.91         0.39         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-7579 
        5.46        30.35        27.45        12.43        18.25        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       30.41        19.76         6.51         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
       14.96         4.93        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 
       20.94        13.32        18.74         0.26        14.47        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       13.55        29.95        71.24        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       34.36        56.65        35.24        29.92        21.11        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       10.22        96.82        37.94        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       66.54        56.91        50.33        48.49        42.64         3.19 
TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       35.90        23.57        52.67        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW 
       11.34        25.28        89.29        78.28        16.37        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       34.59        16.96        43.10        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        2.01         0.92        43.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         1.02         7.07        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 
       25.97        40.01        22.98         4.04        22.98        30.02 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       54.08         4.01        49.05         2.73         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       13.35        16.18        14.73        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       23.28        11.18       140.09         0.49        73.22        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
      106.95         0.16        46.78         6.51        86.76        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 
      156.66        12.59        53.92        39.09        17.72        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 
       26.40        27.39         6.97        66.51        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       36.36       126.18       150.25        22.29         5.92        61.94 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       27.62        38.86        40.24         6.41        36.53        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       31.30        32.91         1.38        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 
       19.04        24.13        31.56        26.79        10.09        13.22 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       16.77         5.29         3.09        32.71         2.01        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        7.76        36.59        38.14        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       30.28        34.13        19.86        24.36        30.48        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       27.16        16.21        14.96        15.29        29.92        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
        3.65        24.92         2.93        11.77        20.22        22.62 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
        2.70         4.01         5.26         2.30         4.01         5.03 
TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       26.63        17.69        71.01        18.31        17.46        27.68 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B 
       21.44        30.81        21.34        27.16        18.15         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       27.02        20.32        18.58        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       13.41        11.84         4.54        64.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HT 
       13.74         4.21         2.89        49.28        25.32        26.43 
TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       83.57        33.07         3.72        12.72        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.03               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            173.82             156.66 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             21.70              21.93 
[1] "0.0 - 173.8 (21.7)" "0.1 - 156.7 (21.9)"
[1] "hr=" "1"  
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         0       13       25        1        15        14
  16P GAIN WILD-TYPE       2       76      127        1        50        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  16P GAIN MUTATED           0         12          5        1
  16P GAIN WILD-TYPE         3         51         14        6
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 13                 76
  STAGE IB                 25                127
  STAGE II                  1                  1
  STAGE IIA                15                 50
  STAGE IIB                14                 81
  STAGE III                 0                  3
  STAGE IIIA               12                 51
  STAGE IIIB                5                 14
  STAGE IV                  1                  6
[1] 10  2
[1] 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    16  53  14   3
  16P GAIN WILD-TYPE  96 241  57  21
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               16                 96
  T2               53                241
  T3               14                 57
  T4                3                 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                  N0  N1  N2  N3
  16P GAIN MUTATED    51  24   8   2
  16P GAIN WILD-TYPE 266 109  32   3
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               51                266
  N1               24                109
  N2                8                 32
  N3                2                  3
[1] 4 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    76   1
  16P GAIN WILD-TYPE 335   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     76    1
  16P GAIN WILD-TYPE  335    6
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               76                335
  1                1                  6
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    17  69
  16P GAIN WILD-TYPE 113 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     17   69
  16P GAIN WILD-TYPE  113  302
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               17                113
  MALE                 69                302
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    59   9
  16P GAIN WILD-TYPE 325  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     59    9
  16P GAIN WILD-TYPE  325   44
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                59                325
  YES                9                 44
[1] 2 2
[1] FALSE
D28V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                       1
  16P GAIN WILD-TYPE                                    14
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  16P GAIN MUTATED                                        1
  16P GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                         1
  16P GAIN WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                            83
  16P GAIN WILD-TYPE                                                         396
D28V10, multiclass
                                                             clus
vv                                                            16P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               83
                                                             clus
vv                                                            16P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                396
[1] 4 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    67   1   0   4
  16P GAIN WILD-TYPE 332  11   4  19
D28V13, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               67                332
  R1                1                 11
  R2                0                  4
  RX                4                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       2                         3    64
  16P GAIN WILD-TYPE     7                        28   285
D28V14, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                   64                285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  60
  16P GAIN WILD-TYPE   7 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   60
  16P GAIN WILD-TYPE    7  257
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               60                257
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    47  36
  16Q GAIN WILD-TYPE 233 178
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                83                411 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                36                178 
$`16Q GAIN MUTATED`
TCGA-18-5595 TCGA-22-1017 TCGA-33-4532 TCGA-43-5668 TCGA-43-A56V TCGA-56-8305 
       27.19        48.82       129.01        18.38        12.03         3.45 
TCGA-56-8504 TCGA-77-A5GA TCGA-98-8020 TCGA-J1-A4AH TCGA-NC-A5HM TCGA-18-3412 
       16.77        42.08         2.76        19.10        39.85        11.34 
TCGA-18-3414 TCGA-21-1071 TCGA-21-1072 TCGA-21-1079 TCGA-21-5783 TCGA-21-5786 
       23.54        46.88        99.16        31.73        88.11        33.93 
TCGA-21-5787 TCGA-22-1011 TCGA-22-4593 TCGA-33-4566 TCGA-33-4587 TCGA-33-AASD 
       10.82         1.74        35.08       173.82        54.44       110.99 
TCGA-34-5241 TCGA-34-7107 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4133 TCGA-37-4135 
       16.93         1.12        26.43        33.90         7.82         6.81 
TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
        0.39        37.58        21.70        71.18        55.56        40.21 
TCGA-43-6143 TCGA-43-A475 TCGA-46-3769 TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 
       22.98         9.73         4.44         8.75        28.96        21.90 
TCGA-56-7223 TCGA-56-8304 TCGA-56-A4BW TCGA-58-8386 TCGA-58-A46K TCGA-60-2706 
       14.53         3.48        19.23         0.03        34.36        92.71 
TCGA-60-2708 TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-A5MV 
       80.45        29.85        26.83        11.77        70.13        36.16 
TCGA-66-2737 TCGA-66-2756 TCGA-66-2768 TCGA-66-2781 TCGA-66-2791 TCGA-70-6722 
        2.01         0.99         2.01         3.98         5.03        12.07 
TCGA-70-6723 TCGA-77-7465 TCGA-77-8009 TCGA-77-A5G1 TCGA-77-A5GF TCGA-85-6175 
       12.33        32.55        55.73       132.36        27.62         9.67 
TCGA-85-6560 TCGA-85-7843 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
       41.39         1.15        34.52        10.09         0.76        22.45 
TCGA-85-8352 TCGA-85-A510 TCGA-85-A53L TCGA-90-A59Q TCGA-92-7341 TCGA-98-8022 
        5.29        15.85        12.39        10.59         3.48        30.67 
TCGA-98-A53B TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-NK-A5CX 
        2.01        20.71        13.18        13.41         3.65 

$`16Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 
       32.19        14.93        60.66        64.93        22.06       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 
        1.55        19.76        31.50        28.96        31.27        17.88 
TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 
       22.49         7.76        78.18         2.93        11.61        19.99 
TCGA-56-8201 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       13.05        17.00        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 
       41.42         9.01        35.34        32.32        66.61         8.02 
TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       20.78        30.81         9.50        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D 
       18.38        16.14        57.07        19.36         5.69        21.21 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE 
        0.07        76.80        40.90        65.65        16.80         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
        8.58        75.75       117.57        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1075 
       86.96         2.79       154.32        49.94       119.54        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       60.89        34.78        15.58       122.43         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       43.23        31.63        41.69        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
       64.21        14.10        27.02        20.48        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
        0.56        38.17        34.75        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       86.30        71.34        79.20        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       62.86        56.32        16.64        97.94        79.53       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      151.27        14.07        63.35         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
        6.94        44.19       118.36        27.16         2.63        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       32.88        65.23        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 
       50.66        44.75        39.32         4.96        38.79         4.04 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        4.01         0.43         0.39         7.96         8.12         7.46 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        3.39       133.25       126.58       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       36.39        68.38        17.06        38.66        39.12        33.11 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       13.38        11.77        14.20        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.83        10.65        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 
       28.34         5.46        30.35        27.45        12.43        18.25 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       18.48        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 
       17.49        33.24        14.96         4.93        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
       20.25        15.81        20.94        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
       14.47        13.25        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       34.78        85.12        56.65        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 
       12.23        10.22        96.82        37.94        21.93        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       66.54        56.91        50.33        48.49        42.64         3.19 
TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       35.90        23.57        52.67        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW 
       11.34        25.28        89.29        78.28        16.37        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       34.59        16.96        43.10        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        2.01         0.92        43.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
        2.01         1.02         2.01         7.07        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
        3.02         2.01        19.00        12.03        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1.97        25.97        40.01        22.98         4.04        22.98 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
       30.02        10.06        54.08         4.01        49.05         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
        6.64         6.94        13.35        16.18        14.73        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       73.12        75.09        23.28        11.18       140.09         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
       73.22        70.13       106.95         0.16        46.78         6.51 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       86.76        37.81       156.66        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       17.72       104.09        11.54        26.40        27.39         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       66.51        54.41        65.49        60.53        36.36       126.18 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6561 
      150.25        22.29         5.92        61.94        38.86        40.24 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
        6.41        36.53        34.95        31.30        32.91         1.38 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       29.95        18.94        25.15        19.04        24.13        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
       26.79        30.64        13.22        16.77         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01        15.39         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
       18.08        22.59        30.28        34.13        30.97        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
       24.36        30.48        19.73        27.16        16.21        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
       15.29        29.92         3.65        24.92         2.93        11.77 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       20.22        22.62         2.70         4.01         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        26.63        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 
       18.31        17.46        27.68        21.44        30.81        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
       27.16        18.15        27.02        20.32        18.58        12.89 
TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       16.11        11.84         4.54        64.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21         2.89        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       14.73        26.43        83.57        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.03               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            173.82             156.66 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             19.23              22.06 
[1] "0.0 - 173.8 (19.2)" "0.1 - 156.7 (22.1)"
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0       10       26        1        17        12
  16Q GAIN WILD-TYPE       2       79      126        1        48        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  16Q GAIN MUTATED           0         13          3        2
  16Q GAIN WILD-TYPE         3         50         16        5
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 10                 79
  STAGE IB                 26                126
  STAGE II                  1                  1
  STAGE IIA                17                 48
  STAGE IIB                12                 83
  STAGE III                 0                  3
  STAGE IIIA               13                 50
  STAGE IIIB                3                 16
  STAGE IV                  2                  5
[1] 10  2
[1] 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    14  53  13   5
  16Q GAIN WILD-TYPE  98 241  58  19
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               14                 98
  T2               53                241
  T3               13                 58
  T4                5                 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
  16Q GAIN MUTATED    51  26   6   1
  16Q GAIN WILD-TYPE 266 107  34   4
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               51                266
  N1               26                107
  N2                6                 34
  N3                1                  4
[1] 4 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    72   2
  16Q GAIN WILD-TYPE 339   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     72    2
  16Q GAIN WILD-TYPE  339    5
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               72                339
  1                2                  5
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    13  72
  16Q GAIN WILD-TYPE 117 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     13   72
  16Q GAIN WILD-TYPE  117  299
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               13                117
  MALE                 72                299
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    59  10
  16Q GAIN WILD-TYPE 325  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     59   10
  16Q GAIN WILD-TYPE  325   43
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                59                325
  YES               10                 43
[1] 2 2
[1] FALSE
D29V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                       2
  16Q GAIN WILD-TYPE                                    13
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  16Q GAIN MUTATED                                        1
  16Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                         1
  16Q GAIN WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                            81
  16Q GAIN WILD-TYPE                                                         398
D29V10, multiclass
                                                             clus
vv                                                            16Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               81
                                                             clus
vv                                                            16Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                398
[1] 4 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   3   0   4
  16Q GAIN WILD-TYPE 330   9   4  19
D29V13, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               69                330
  R1                3                  9
  R2                0                  4
  RX                4                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       4                         5    61
  16Q GAIN WILD-TYPE     5                        26   288
D29V14, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                5                 26
  WHITE                                   61                288
[1] 3 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     1  63
  16Q GAIN WILD-TYPE   7 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   63
  16Q GAIN WILD-TYPE    7  254
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               63                254
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    31  32
  17P GAIN WILD-TYPE 249 182
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                63                431 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                182 
$`17P GAIN MUTATED`
TCGA-22-1017 TCGA-33-4532 TCGA-43-2578 TCGA-43-7657 TCGA-43-8118 TCGA-56-8201 
       48.82       129.01        22.49         7.76         2.93        13.05 
TCGA-56-8308 TCGA-56-8504 TCGA-68-8250 TCGA-77-A5GA TCGA-94-7557 TCGA-94-7943 
       17.00        16.77         8.02        42.08         0.16        18.38 
TCGA-98-8020 TCGA-J1-A4AH TCGA-18-3412 TCGA-18-3417 TCGA-21-1071 TCGA-21-1072 
        2.76        19.10        11.34        36.07        46.88        99.16 
TCGA-22-4593 TCGA-22-4601 TCGA-22-4613 TCGA-22-5474 TCGA-33-4538 TCGA-33-4582 
       35.08        34.75        11.77        14.63        97.94       103.53 
TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-5240 TCGA-34-5241 TCGA-56-7222 
      110.99       118.36         2.63        50.66        16.93        18.48 
TCGA-56-7582 TCGA-56-7730 TCGA-58-8391 TCGA-58-A46K TCGA-60-2726 TCGA-63-A5ML 
       19.76         6.51        71.24        34.36        11.77        45.57 
TCGA-66-2770 TCGA-66-2787 TCGA-66-2792 TCGA-68-8251 TCGA-70-6723 TCGA-77-7142 
       23.01        40.01        30.02        13.35        12.33        73.22 
TCGA-77-8156 TCGA-77-A5GF TCGA-85-7843 TCGA-85-7950 TCGA-85-8277 TCGA-85-8350 
       36.36        27.62         1.15        18.94        10.09        22.45 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8664 TCGA-85-A510 TCGA-85-A5B5 
        5.29         3.09        32.71        18.08        15.85         3.65 
TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 TCGA-96-8169 TCGA-98-A53I TCGA-L3-A524 
       11.77        22.62         2.70        18.31        18.58        16.11 
TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HL 
       11.84         1.22         2.89 

$`17P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       27.19        32.19        14.93        60.66        64.93        22.06 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      133.74         1.55        19.76        31.50        28.96        31.27 
TCGA-39-5039 TCGA-43-5668 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       17.88        18.38        78.18        11.61        12.03        19.99 
TCGA-56-8305 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
        3.45        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GB 
        9.01        35.34        32.32        66.61        20.78        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
        9.50        14.07        21.04        16.14        57.07        19.36 
TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
        5.69        21.21         0.07        76.80        39.85        40.90 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       65.65        16.80         0.43         8.58        75.75       117.57 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       23.54        92.15        92.42        86.96         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       49.94       119.54        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       31.73       122.43         9.34       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
       88.11        41.69        33.93        10.82        21.99         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
        4.31        64.21         1.74        14.10        27.02        20.48 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 
       48.33        24.13         0.56        38.17        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       19.30         9.57        63.55        44.25         0.79        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       71.34        79.20        11.74        18.84        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
       56.32        16.64        79.53       173.82       151.27        14.07 
TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       54.44        63.35         4.70         0.30        36.62         6.94 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       44.19        27.16        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       74.66         9.07        60.30        44.75        39.32         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        38.79         4.04        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         7.96         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        6.81         0.39         3.39        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1.71        24.33         1.94        60.53        36.39        68.38 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       71.18        55.56        17.06        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       33.11        27.91        22.98        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        3.81        19.59        13.38        11.77         9.73        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
       13.32        12.16        13.02         9.83         4.44        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       13.91         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       30.35         8.75        27.45        28.96        12.43        18.25 
TCGA-56-6545 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 
       21.90        14.53        31.27        30.41         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       33.24        14.96         4.93         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK 
       20.25        15.81        20.94        19.23        13.32        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26        14.47         0.03        13.25        13.55        29.95 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       16.47        34.78        85.12        56.65        35.24        29.92 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       21.11        12.23        10.22        96.82        37.94        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       21.93        80.45        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       48.49        42.64         3.19        29.85        35.90        23.57 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       26.83        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN 
      102.67        70.62        58.65        59.97        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       25.28        89.29        78.28        16.37        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       34.59        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        1.02         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       25.05         0.99         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        7.07        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 
        3.98        12.00        24.95         1.97        25.97        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
        4.04        22.98         5.03        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J 
       49.05         2.73         6.64         6.94        16.18        14.73 
TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.07        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
      140.09         0.49        70.13       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       32.55         6.51        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       12.59        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       26.40        27.39         6.97        66.51        54.41        65.49 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       60.53       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
       61.94        38.86         9.67        41.39        40.24         6.41 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
       36.53        34.95        31.30        32.91         1.38        29.95 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
       25.15        19.04        24.13        31.56        26.79        30.64 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8355 TCGA-85-8479 
       34.52         0.76        13.22        16.77         2.01        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL 
        7.76        36.59        38.14        12.59        22.59        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       34.13        30.97        19.86        24.36        30.48        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       27.16        16.21        14.96        15.29        29.92        12.39 
TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
       24.92         2.93        20.22        10.59         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        5.26         2.30         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       17.69        71.01        17.46        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.67        21.34        27.16        18.15         2.01        27.02 
TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF 
       20.32        20.71        12.89        13.18        13.41         4.54 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO 
       64.54        57.30        13.74         4.21        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       25.32        14.73        26.43        83.57         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        12.72        43.89        11.18         0.20 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.16               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            129.01             173.82 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             18.38              22.59 
[1] "0.2 - 129.0 (18.4)" "0.0 - 173.8 (22.6)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         0       14       20        0        11        11
  17P GAIN WILD-TYPE       2       75      132        2        54        84
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  17P GAIN MUTATED           0          8          0        1
  17P GAIN WILD-TYPE         3         55         19        6
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 14                 75
  STAGE IB                 20                132
  STAGE II                  0                  2
  STAGE IIA                11                 54
  STAGE IIB                11                 84
  STAGE III                 0                  3
  STAGE IIIA                8                 55
  STAGE IIIB                0                 19
  STAGE IV                  1                  6
[1] 10  2
[1] 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    14  43   7   1
  17P GAIN WILD-TYPE  98 251  64  23
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               14                 98
  T2               43                251
  T3                7                 64
  T4                1                 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                  N0  N1  N2  N3
  17P GAIN MUTATED    42  18   4   0
  17P GAIN WILD-TYPE 275 115  36   5
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               42                275
  N1               18                115
  N2                4                 36
  N3                0                  5
[1] 4 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    51   1
  17P GAIN WILD-TYPE 360   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     51    1
  17P GAIN WILD-TYPE  360    6
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               51                360
  1                1                  6
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    14  51
  17P GAIN WILD-TYPE 116 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     14   51
  17P GAIN WILD-TYPE  116  320
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               14                116
  MALE                 51                320
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    55   6
  17P GAIN WILD-TYPE 329  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     55    6
  17P GAIN WILD-TYPE  329   47
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                55                329
  YES                6                 47
[1] 2 2
[1] FALSE
D30V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED                                       3
  17P GAIN WILD-TYPE                                    12
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  17P GAIN MUTATED                                        1
  17P GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED                                         0
  17P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                            61
  17P GAIN WILD-TYPE                                                         418
D30V10, multiclass
                                                             clus
vv                                                            17P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               61
                                                             clus
vv                                                            17P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                418
[1] 4 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    47   3   0   4
  17P GAIN WILD-TYPE 352   9   4  19
D30V13, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               47                352
  R1                3                  9
  R2                0                  4
  RX                4                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       1                         5    49
  17P GAIN WILD-TYPE     8                        26   300
D30V14, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                5                 26
  WHITE                                   49                300
[1] 3 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     2  45
  17P GAIN WILD-TYPE   6 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2   45
  17P GAIN WILD-TYPE    6  272
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               45                272
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    85  70
  17Q GAIN WILD-TYPE 195 144
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               155                339 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                70                144 
$`17Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-22-1017 TCGA-22-5471 TCGA-33-4532 TCGA-34-2604 
        4.47         4.80        48.82        60.66       129.01        31.50 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-8118 TCGA-56-8201 TCGA-56-8308 
       22.49        18.38         7.76         2.93        13.05        17.00 
TCGA-56-8504 TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-94-A5I4 
       16.77        35.34        66.61         8.02        42.08        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE 
       57.07        19.36        19.10        39.85        40.90         0.43 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      117.57        11.34        36.07        46.88        99.16        70.16 
TCGA-21-1077 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-1012 
       34.78       119.80        43.23        33.93        10.82        14.10 
TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4613 TCGA-22-5473 
       35.08        38.17        34.75        13.12        11.77        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5483 TCGA-33-4538 TCGA-33-4582 TCGA-33-4586 
       14.63        44.25        18.84        97.94       103.53        14.07 
TCGA-33-6738 TCGA-33-AASJ TCGA-34-2596 TCGA-34-5231 TCGA-34-5240 TCGA-34-8456 
       63.35       118.36         2.63        65.23        50.66        26.43 
TCGA-37-3792 TCGA-37-4133 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 
        0.39         7.82        37.58        21.70       126.58       111.35 
TCGA-39-5027 TCGA-39-5037 TCGA-43-2576 TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 
      102.18        55.56        40.21         9.73         9.83        10.65 
TCGA-46-6026 TCGA-51-4080 TCGA-52-7812 TCGA-56-1622 TCGA-56-7222 TCGA-56-7223 
       13.91         0.39        27.45        28.96        18.48        14.53 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8629 TCGA-56-A4BX TCGA-58-8386 
       19.76         6.51         3.48        15.81        13.32         0.03 
TCGA-58-8391 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N TCGA-60-2703 TCGA-60-2706 
       71.24        85.12        34.36        29.92        96.82        92.71 
TCGA-60-2707 TCGA-60-2722 TCGA-60-2726 TCGA-63-6202 TCGA-63-A5MB TCGA-63-A5MJ 
       21.93        29.85        11.77        52.67       102.67        59.97 
TCGA-63-A5ML TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2742 TCGA-66-2756 TCGA-66-2758 
       45.57        36.16        53.88        21.07         0.99        21.01 
TCGA-66-2763 TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 
        0.99         2.01        23.01         3.02         2.01         3.98 
TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-68-7755 TCGA-68-8251 
       40.01         5.03        30.02        10.06         2.73        13.35 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       12.33        29.56        23.28        11.18       140.09         0.49 
TCGA-77-7142 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8136 
       73.22        32.55         6.51        55.73        37.81        39.09 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-6560 
       36.36       150.25        22.29         5.92        27.62        41.39 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8070 TCGA-85-8277 TCGA-85-8350 TCGA-85-8352 
        1.15        29.95        31.56        10.09        22.45         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QR 
        3.09        32.71        18.08        22.59        30.28        19.73 
TCGA-85-A510 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       15.85         2.93        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-96-8169 TCGA-98-8023 TCGA-98-A53I TCGA-98-A53J 
        2.70         3.48        18.31        21.34        18.58        20.71 
TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HL TCGA-NK-A5CR TCGA-O2-A52N 
       16.11        11.84         2.89        83.57        33.07 

$`17Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19        31.99         6.18        27.19        32.19 
TCGA-22-1000 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 
       14.93        64.93        22.06       133.74         1.55        19.76 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V 
       28.96        31.27        17.88        78.18        11.61        12.03 
TCGA-56-7221 TCGA-56-8305 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       19.99         3.45        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 
       41.42         9.01        32.32        20.78        30.81         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-98-8020 TCGA-98-A539 
       14.07        21.04         0.16        18.38         2.76         5.69 
TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W 
       21.21         0.07        76.80        65.65        16.80         8.58 
TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       75.75        23.54        92.15        92.42        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
      154.32        49.94       119.54        60.89        15.58        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 
      122.43         9.34        31.63        88.11        41.69        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 
        7.33         4.31        64.21         1.74        27.02        20.48 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       48.33        24.13         0.56        32.02        19.30         9.57 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 
        0.79        86.30        71.34        79.20        11.74        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
       62.86        56.32        16.64        79.53       173.82       151.27 
TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       54.44         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
       44.19        27.16        61.61        32.88        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
        9.07        60.30        16.93        44.75        39.32         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        1.12        38.79         4.04        33.90         4.01         0.43 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        7.96         8.12         7.46         6.81         0.39         3.39 
TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
      133.25        68.58        55.20        82.52         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 
        1.94        60.53        36.39        68.38        71.18        17.06 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       38.66        39.12        33.11        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       21.47         5.46         3.81        19.59        13.38        11.77 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-51-4079 
       14.20        13.32        12.16        13.02         4.44         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-5897 
       29.95        28.34         5.46        30.35         8.75        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 
       18.25        21.90        31.27        30.41         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       33.24        14.96         4.93        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75        13.81        10.36         9.93        20.25 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 
       20.94        19.23        18.74         0.26        14.47        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M 
       13.55        29.95        16.47        34.78        56.65        35.24 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 
       21.11        12.23        10.22        37.94        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       66.54        56.91        50.33        48.49        42.64         3.19 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       35.90        23.57        26.83        70.13        70.42        68.15 
TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       55.30        70.62        58.65        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       89.29        78.28        16.37        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
        2.01         0.99         1.02         2.01         0.92        43.99 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
       25.05         2.01         1.02         2.01         7.07        19.00 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       19.00        12.03        12.00        24.95         1.97        25.97 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
       22.98         4.04        22.98        54.08         4.01        49.05 
TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 
        6.64         6.94        16.18        14.73        12.07        73.12 
TCGA-77-6844 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 
       75.09        70.13       106.95         0.16        46.78        86.76 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
      156.66        12.59        53.92        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       26.40        27.39         6.97        66.51        54.41        65.49 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 
       60.53       126.18       132.36        61.94        38.86         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       40.24         6.41        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
        1.38        18.94        25.15        19.04        24.13        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8355 
       30.64        34.52         0.76        13.22        16.77         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CN 
       15.39         7.76        36.59        38.14        12.59        34.13 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z 
       30.97        19.86        24.36        30.48        27.16        16.21 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       14.96        15.29        29.92        12.39         3.65        24.92 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         5.26         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       14.14        17.69        71.01        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.81        30.67        27.16        18.15         2.01        27.02 
TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG 
       20.32        12.89        13.18        13.41         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO 
        1.22        57.30        13.74         4.21        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S 
       25.32        14.73        26.43         3.65         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.03               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            150.25             173.82 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             22.29              21.44 
[1] "0.0 - 150.2 (22.3)" "0.1 - 173.8 (21.4)"
[1] "hr=" "1"  
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         1       20       48        0        28        31
  17Q GAIN WILD-TYPE       1       69      104        2        37        64
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  17Q GAIN MUTATED           0         18          7        3
  17Q GAIN WILD-TYPE         3         45         12        4
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 20                 69
  STAGE IB                 48                104
  STAGE II                  0                  2
  STAGE IIA                28                 37
  STAGE IIB                31                 64
  STAGE III                 0                  3
  STAGE IIIA               18                 45
  STAGE IIIB                7                 12
  STAGE IV                  3                  4
[1] 10  2
[1] 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    26 109  16   7
  17Q GAIN WILD-TYPE  86 185  55  17
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               26                 86
  T2              109                185
  T3               16                 55
  T4                7                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q GAIN MUTATED    89  53  13   2
  17Q GAIN WILD-TYPE 228  80  27   3
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               89                228
  N1               53                 80
  N2               13                 27
  N3                2                  3
[1] 4 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   130   3
  17Q GAIN WILD-TYPE 281   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    130    3
  17Q GAIN WILD-TYPE  281    4
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0              130                281
  1                3                  4
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    26 132
  17Q GAIN WILD-TYPE 104 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     26  132
  17Q GAIN WILD-TYPE  104  239
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               26                104
  MALE                132                239
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   119  19
  17Q GAIN WILD-TYPE 265  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    119   19
  17Q GAIN WILD-TYPE  265   34
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO               119                265
  YES               19                 34
[1] 2 2
[1] FALSE
D31V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED                                       6
  17Q GAIN WILD-TYPE                                     9
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  17Q GAIN MUTATED                                        1
  17Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED                                         0
  17Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                           151
  17Q GAIN WILD-TYPE                                                         328
D31V10, multiclass
                                                             clus
vv                                                            17Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              151
                                                             clus
vv                                                            17Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                328
[1] 4 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   123   5   2   6
  17Q GAIN WILD-TYPE 276   7   2  17
D31V13, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0              123                276
  R1                5                  7
  R2                2                  2
  RX                6                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       2                         5   111
  17Q GAIN WILD-TYPE     7                        26   238
D31V14, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                5                 26
  WHITE                                  111                238
[1] 3 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     4  94
  17Q GAIN WILD-TYPE   4 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   94
  17Q GAIN WILD-TYPE    4  223
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               94                223
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    81  64
  18P GAIN WILD-TYPE 199 150
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               145                349 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                64                150 
$`18P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-4083 TCGA-22-5471 TCGA-33-4532 TCGA-34-2604 
        4.47        31.99         6.18        60.66       129.01        31.50 
TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-A4BY 
       22.49         7.76        78.18         2.93        11.61        17.85 
TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 TCGA-94-A5I4 TCGA-96-7545 TCGA-J1-A4AH 
        0.13        41.42         9.01        16.14        57.07        19.10 
TCGA-18-3411 TCGA-18-3412 TCGA-21-1075 TCGA-21-1079 TCGA-21-1082 TCGA-21-5783 
      117.57        11.34        70.16        31.73       119.80        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-4591 TCGA-22-4595 TCGA-22-4604 
       41.69        33.93         7.33        20.48        24.13        13.12 
TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4566 TCGA-33-4586 
       71.34        18.84        62.86        56.32       173.82        14.07 
TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 
      110.99        44.19         2.63        65.23         9.07        60.30 
TCGA-34-5240 TCGA-37-3792 TCGA-37-4141 TCGA-37-A5EL TCGA-39-5016 TCGA-39-5019 
       50.66         0.39         0.39        37.58       126.58       111.35 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 TCGA-39-5040 
       68.58       102.18        24.33        60.53        55.56        17.06 
TCGA-43-2576 TCGA-43-5670 TCGA-43-A475 TCGA-46-6026 TCGA-51-4081 TCGA-52-7811 
       40.21        27.91         9.73        13.91        29.95         8.75 
TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-8304 TCGA-56-8309 
       18.25        14.53        30.41         6.51         3.48        14.07 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8386 TCGA-58-8391 TCGA-58-8392 
       20.94        13.32         0.26         0.03        71.24        16.47 
TCGA-58-A46N TCGA-60-2698 TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
       29.92        10.22        29.85        26.83        11.77        70.13 
TCGA-63-7023 TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MW TCGA-66-2734 TCGA-66-2758 
       55.30        58.65        45.57        53.88        43.10        21.01 
TCGA-66-2759 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2783 
       25.05         2.01         7.07        23.01         2.01        24.95 
TCGA-66-2787 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J 
       40.01        10.06        54.08        49.05         2.73        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6845 TCGA-77-7335 TCGA-77-7463 TCGA-77-7465 
       12.07        12.33        23.28        70.13        46.78        32.55 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8143 TCGA-77-8150 TCGA-77-8153 
       55.73        37.81       156.66        26.40        54.41        65.49 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7843 
       36.36       150.25        27.62        40.24         6.41         1.15 
TCGA-85-7844 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 
       29.95        19.04        31.56        26.79        34.52        10.09 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN 
        5.29         3.09        32.71        18.08        22.59        34.13 
TCGA-85-A4JB TCGA-85-A50M TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE 
       30.97        27.16        15.85         3.65        11.77        22.62 
TCGA-90-A59Q TCGA-92-8064 TCGA-94-A4VJ TCGA-98-8021 TCGA-98-A53I TCGA-L3-A4E7 
       10.59         5.26        14.14        30.81        18.58        12.89 
TCGA-L3-A524 TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52N 
       16.11        57.30         2.89        14.73         3.65        33.07 
TCGA-O2-A5IB 
       11.18 

$`18P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20       123.19         4.80        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 
       48.82        64.93        22.06       133.74         1.55        19.76 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-A56V TCGA-56-7221 
       28.96        31.27        17.88        18.38        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-60-2696 
       13.05         3.45        17.00        16.77        21.04         3.58 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
       35.34        32.32        66.61         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       30.81         9.50        14.07        21.04         0.16        18.38 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE 
       19.36         2.76         5.69        21.21         0.07        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
       39.85        40.90        65.65        16.80         0.43         8.58 
TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       75.75        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2.79       154.32        49.94       119.54        46.88        99.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
       60.89        34.78        15.58       122.43         9.34        43.23 
TCGA-21-5782 TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       31.63        10.82        21.99         4.31        64.21         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       14.10        27.02        35.08        48.33         0.56        38.17 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       34.75        32.02        19.30         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 
       14.63        44.25         0.79        86.30        79.20        11.74 
TCGA-22-5485 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 
       30.12        16.64        97.94        79.53       103.53       151.27 
TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       54.44        63.35         4.70         0.30        36.62         6.94 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
      118.36        27.16        61.61        32.88        81.24        74.66 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        44.75        39.32         4.96         1.12        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
        4.04        26.43        33.90         4.01         0.43         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EN 
        8.12         7.46         7.82         6.81         3.39        21.70 
TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 
      133.25        55.20        82.52         1.71         1.94        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 
       68.38        71.18        38.66        39.12        33.11        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       11.77        14.20        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 
        4.44        10.65         0.39         0.39        28.34         5.46 
TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 
       30.35        27.45        28.96        12.43        21.90        18.48 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       31.27        19.76         0.10        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8307 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
        4.93        26.89         1.35         1.81        22.75        13.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK 
       10.36         9.93        20.25        15.81        19.23        18.74 
TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J 
       14.47        13.25        13.55        29.95        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 
       34.36        56.65        35.24        21.11        12.23        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 
       56.91        50.33        48.49        42.64         3.19        35.90 
TCGA-60-2724 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG 
       23.57        52.67        70.42        68.15       102.67        70.62 
TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       59.97        14.99        11.34        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 
       16.37        36.16        34.59        16.96         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        0.99         1.02         2.01         0.92         0.99        43.99 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 
        0.99         2.01         1.02         2.01        19.00         3.02 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 
       19.00        12.03         3.98        12.00         1.97        25.97 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 
       22.98         4.04        22.98         5.03        30.02         4.01 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
        6.64         6.94        13.35        16.18        29.56        73.12 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 
       75.09        11.18       140.09         0.49        73.22       106.95 
TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        0.16         6.51        86.76        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       17.72       104.09        11.54        27.39         6.97        66.51 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       60.53       126.18       132.36        22.29         5.92        61.94 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       38.86         9.67        41.39        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 TCGA-85-8072 
       32.91         1.38        18.94        25.15        24.13        30.64 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8355 TCGA-85-8479 
        0.76        13.22        22.45        16.77         2.01        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JC 
        7.76        36.59        38.14        12.59        30.28        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
       24.36        30.48        19.73        16.21        14.96        15.29 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-92-7340 
       29.92        12.39        24.92         2.93        20.22         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        3.48         4.01         2.30         4.01         5.03        26.63 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       17.69        71.01        18.31        17.46        27.68        21.44 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.67        21.34        27.16        18.15         2.01        27.02 
TCGA-98-A53H TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       20.32        20.71        13.18        13.41        11.84         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO 
       64.54         1.22        13.74         4.21        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       25.32        26.43        83.57         3.72        12.72        43.89 
TCGA-XC-AA0X 
        0.20 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.03               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            173.82             154.32 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             24.95              21.04 
[1] "0.0 - 173.8 (24.9)" "0.1 - 154.3 (21.0)"
[1] "hr=" "1.1"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         1       21       43        0        25        25
  18P GAIN WILD-TYPE       1       68      109        2        40        70
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  18P GAIN MUTATED           1         23          7        1
  18P GAIN WILD-TYPE         2         40         12        6
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 21                 68
  STAGE IB                 43                109
  STAGE II                  0                  2
  STAGE IIA                25                 40
  STAGE IIB                25                 70
  STAGE III                 1                  2
  STAGE IIIA               23                 40
  STAGE IIIB                7                 12
  STAGE IV                  1                  6
[1] 10  2
[1] 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    28  94  20   6
  18P GAIN WILD-TYPE  84 200  51  18
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               28                 84
  T2               94                200
  T3               20                 51
  T4                6                 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
  18P GAIN MUTATED    84  44  16   2
  18P GAIN WILD-TYPE 233  89  24   3
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               84                233
  N1               44                 89
  N2               16                 24
  N3                2                  3
[1] 4 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   123   1
  18P GAIN WILD-TYPE 288   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    123    1
  18P GAIN WILD-TYPE  288    6
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0              123                288
  1                1                  6
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    33 115
  18P GAIN WILD-TYPE  97 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     33  115
  18P GAIN WILD-TYPE   97  256
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               33                 97
  MALE                115                256
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   110  24
  18P GAIN WILD-TYPE 274  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    110   24
  18P GAIN WILD-TYPE  274   29
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO               110                274
  YES               24                 29
[1] 2 2
[1] FALSE
D32V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                       3
  18P GAIN WILD-TYPE                                    12
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  18P GAIN MUTATED                                        1
  18P GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                         0
  18P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                           144
  18P GAIN WILD-TYPE                                                         335
D32V10, multiclass
                                                             clus
vv                                                            18P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              144
                                                             clus
vv                                                            18P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                335
[1] 4 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   117   3   3   8
  18P GAIN WILD-TYPE 282   9   1  15
D32V13, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0              117                282
  R1                3                  9
  R2                3                  1
  RX                8                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       4                         3   109
  18P GAIN WILD-TYPE     5                        28   240
D32V14, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                  109                240
[1] 3 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     2  95
  18P GAIN WILD-TYPE   6 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   95
  18P GAIN WILD-TYPE    6  222
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               95                222
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    53  48
  18Q GAIN WILD-TYPE 227 166
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               101                393 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                48                166 
$`18Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-4083 TCGA-22-5471 TCGA-33-4532 TCGA-34-2604 TCGA-34-2609 
        4.47         6.18        60.66       129.01        31.50        31.27 
TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-60-2711 TCGA-60-2712 TCGA-96-7545 
       22.49         7.76        78.18        41.42         9.01        57.07 
TCGA-J1-A4AH TCGA-18-3411 TCGA-21-1075 TCGA-21-1082 TCGA-21-5783 TCGA-21-5784 
       19.10       117.57        70.16       119.80        88.11        41.69 
TCGA-22-1012 TCGA-22-4595 TCGA-22-4604 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
       14.10        24.13        13.12         0.79        71.34        79.20 
TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
       18.84        62.86        56.32       173.82       103.53        14.07 
TCGA-34-2596 TCGA-34-5236 TCGA-34-5239 TCGA-34-8456 TCGA-37-4141 TCGA-39-5019 
        2.63         9.07        60.30        26.43         0.39       111.35 
TCGA-39-5021 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 TCGA-39-5040 TCGA-43-3920 
       68.58        24.33        60.53        55.56        17.06        33.11 
TCGA-43-6143 TCGA-43-8115 TCGA-43-A475 TCGA-46-6026 TCGA-51-4081 TCGA-52-7811 
       22.98        13.38         9.73        13.91        29.95         8.75 
TCGA-56-5898 TCGA-56-7580 TCGA-56-7730 TCGA-56-A49D TCGA-56-A4BX TCGA-58-8392 
       18.25        30.41         6.51        20.94        13.32        16.47 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2722 TCGA-60-2725 TCGA-63-7020 TCGA-63-7023 
       29.92        21.11        29.85        26.83        70.13        55.30 
TCGA-63-A5ML TCGA-66-2758 TCGA-66-2759 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 
       45.57        21.01        25.05         7.07        23.01         2.01 
TCGA-66-2787 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-77-7463 
       40.01        10.06        54.08        49.05         2.73        46.78 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8143 TCGA-77-8150 TCGA-77-8153 
       32.55        55.73        37.81        26.40        54.41        65.49 
TCGA-77-8156 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7843 TCGA-85-7950 
       36.36        27.62        40.24         6.41         1.15        18.94 
TCGA-85-8070 TCGA-85-8277 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       31.56        10.09        18.08        22.59        34.13        30.97 
TCGA-85-A50M TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8064 TCGA-98-8021 TCGA-98-A53I 
       27.16        22.62        10.59         5.26        30.81        18.58 
TCGA-L3-A4E7 TCGA-MF-A522 TCGA-NC-A5HL TCGA-NK-A5CX TCGA-O2-A5IB 
       12.89        11.84         2.89         3.65        11.18 

$`18Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19         4.80        31.99        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 
       14.93        48.82        64.93        22.06       133.74         1.55 
TCGA-33-6737 TCGA-34-2605 TCGA-39-5039 TCGA-43-5668 TCGA-43-8118 TCGA-43-A474 
       19.76        28.96        17.88        18.38         2.93        11.61 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       12.03        19.99        13.05         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2715 TCGA-60-2721 
       17.85        21.04         0.13         3.58        35.34        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 
       66.61         8.02        20.78        42.08        30.81         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK 
       14.07        21.04         0.16        18.38        16.14        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        2.76         5.69        21.21         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       40.90        65.65        16.80         0.43         8.58        75.75 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       11.34        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2.79       154.32        49.94       119.54        46.88        99.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       60.89        34.78        15.58        31.73       122.43         9.34 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
       43.23        31.63        33.93        10.82        21.99         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
        4.31        64.21         1.74        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 
       48.33         0.56        38.17        34.75        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
        9.57        11.77        63.55        14.63        44.25        86.30 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 
       11.74        30.12        16.64        97.94        79.53       151.27 
TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       54.44        63.35         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 
      110.99        44.19       118.36        27.16        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       65.23        81.24        74.66        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX 
       39.32         4.96         1.12        38.79         4.04        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        4.01         0.43         0.39         7.96         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        7.82         6.81         3.39        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
      126.58        55.20        82.52       102.18         1.71         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       36.39        68.38        71.18        40.21        38.66        39.12 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       11.77        14.20        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 
        4.44        10.65         0.39         0.39        28.34         5.46 
TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 
       30.35        27.45        28.96        12.43        21.90        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       14.53        31.27        19.76         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       14.96         4.93         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75        13.81        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       15.81        19.23        18.74         0.26        14.47         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
       13.25        13.55        29.95        71.24        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       34.36        56.65        35.24        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 
       56.91        50.33        48.49        42.64         3.19        35.90 
TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB 
       23.57        11.77        52.67        70.42        68.15       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       70.62        58.65        59.97        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       89.29        78.28        16.37        36.16        53.88        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       16.96        43.10         2.01        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 
        2.01         0.92         0.99        43.99         0.99         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 
        1.02         2.01         2.01        19.00         3.02        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       12.03         3.98        12.00        24.95         1.97        25.97 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 
       22.98         4.04        22.98         5.03        30.02         4.01 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        6.64         6.94        13.35        16.18        14.73        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.33        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         0.16 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        6.51        86.76       156.66        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       17.72       104.09        11.54        27.39         6.97        66.51 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       60.53       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 
       61.94        38.86         9.67        41.39        36.53        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 
       31.30        32.91         1.38        29.95        25.15        19.04 
TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
       24.13        26.79        30.64        34.52         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       22.45        16.77         5.29         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL 
       15.39         7.76        36.59        38.14        12.59        30.28 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
       19.86        24.36        30.48        19.73        16.21        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       14.96        15.29        29.92        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
        2.93        11.77        20.22         2.70         3.48         4.01 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        2.30         4.01         5.03        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 
       71.01        18.31        17.46        27.68        21.44        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       21.34        27.16        18.15         2.01        27.02        20.32 
TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG 
       20.71        16.11        13.18        13.41         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO 
        1.22        57.30        13.74         4.21        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q 
       25.32        14.73        26.43        83.57        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       12.72        43.89         0.20 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.39               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            173.82             156.66 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             26.40              20.78 
[1] "0.4 - 173.8 (26.4)" "0.0 - 156.7 (20.8)"
[1] "hr=" "1"  
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         0       14       35        0        19        15
  18Q GAIN WILD-TYPE       2       75      117        2        46        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  18Q GAIN MUTATED           1         13          4        0
  18Q GAIN WILD-TYPE         2         50         15        7
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 14                 75
  STAGE IB                 35                117
  STAGE II                  0                  2
  STAGE IIA                19                 46
  STAGE IIB                15                 80
  STAGE III                 1                  2
  STAGE IIIA               13                 50
  STAGE IIIB                4                 15
  STAGE IV                  0                  7
[1] 10  2
[1] 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  70   8   5
  18Q GAIN WILD-TYPE  93 224  63  19
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               19                 93
  T2               70                224
  T3                8                 63
  T4                5                 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
  18Q GAIN MUTATED    61  30  10   0
  18Q GAIN WILD-TYPE 256 103  30   5
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               61                256
  N1               30                103
  N2               10                 30
  N3                0                  5
[1] 4 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    89   0
  18Q GAIN WILD-TYPE 322   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     89    0
  18Q GAIN WILD-TYPE  322    7
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               89                322
  1                0                  7
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    23  79
  18Q GAIN WILD-TYPE 107 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     23   79
  18Q GAIN WILD-TYPE  107  292
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               23                107
  MALE                 79                292
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    76  16
  18Q GAIN WILD-TYPE 308  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     76   16
  18Q GAIN WILD-TYPE  308   37
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                76                308
  YES               16                 37
[1] 2 2
[1] FALSE
D33V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED                                       3
  18Q GAIN WILD-TYPE                                    12
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  18Q GAIN MUTATED                                        0
  18Q GAIN WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED                                         0
  18Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                            99
  18Q GAIN WILD-TYPE                                                         380
D33V10, multiclass
                                                             clus
vv                                                            18Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               99
                                                             clus
vv                                                            18Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                380
[1] 4 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    83   3   2   3
  18Q GAIN WILD-TYPE 316   9   2  20
D33V13, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               83                316
  R1                3                  9
  R2                2                  2
  RX                3                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       2                         1    76
  18Q GAIN WILD-TYPE     7                        30   273
D33V14, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                1                 30
  WHITE                                   76                273
[1] 3 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     2  64
  18Q GAIN WILD-TYPE   6 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   64
  18Q GAIN WILD-TYPE    6  253
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               64                253
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    64  49
  19P GAIN WILD-TYPE 216 165
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               113                381 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                49                165 
$`19P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-22-5471 TCGA-33-4533 TCGA-33-6737 TCGA-34-2605 
        4.47         4.80        60.66       133.74        19.76        28.96 
TCGA-43-7657 TCGA-60-2712 TCGA-63-A5MH TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
        7.76         9.01        66.61        57.07        19.36         2.76 
TCGA-J1-A4AH TCGA-NC-A5HR TCGA-O2-A52W TCGA-18-3411 TCGA-18-3414 TCGA-18-3421 
       19.10        40.90         8.58       117.57        23.54        86.96 
TCGA-21-5787 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
       10.82         1.74        14.10        20.48        35.08        24.13 
TCGA-22-4604 TCGA-22-5474 TCGA-22-5477 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 
       13.12        14.63        44.25        79.20        18.84        62.86 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4586 TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 
       97.94       173.82        14.07       118.36         2.63        61.61 
TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-7107 TCGA-34-A5IX TCGA-37-A5EL 
       65.23        60.30        50.66         1.12        33.90        37.58 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 
      126.58       111.35        60.53        36.39        68.38        17.06 
TCGA-43-6143 TCGA-43-A475 TCGA-46-3768 TCGA-52-7809 TCGA-52-7810 TCGA-56-7580 
       22.98         9.73         9.83         5.46        30.35        30.41 
TCGA-56-7582 TCGA-56-8304 TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       19.76         3.48        34.78        35.24        29.92        21.11 
TCGA-60-2704 TCGA-60-2708 TCGA-60-2719 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG 
       37.94        80.45        42.64        68.15       102.67        70.62 
TCGA-63-A5ML TCGA-66-2770 TCGA-66-2777 TCGA-66-2787 TCGA-66-2794 TCGA-66-2800 
       45.57        23.01         2.01        40.01        54.08        49.05 
TCGA-68-8251 TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 
       13.35        14.73        12.07        73.12       140.09         0.49 
TCGA-77-7142 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8148 TCGA-77-8150 
       73.22        32.55        86.76        55.73        66.51        54.41 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 
      132.36       150.25         5.92        61.94        27.62         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7843 TCGA-85-7950 TCGA-85-8277 
       40.24         6.41        36.53         1.15        18.94        10.09 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A5B5 
        3.09        32.71        15.39        34.13        19.73         3.65 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 TCGA-98-A53I 
       11.77        22.62        10.59         2.70         5.26        18.58 
TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HL TCGA-NK-A5CX 
       20.71        13.18        13.41         2.89         3.65 

$`19P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19        31.99         6.18        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 
       14.93        48.82        64.93        22.06       129.01         1.55 
TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 
       31.50        31.27        17.88        22.49        18.38        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
        2.93        11.61        12.03        19.99        13.05         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       17.00        16.77        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
       41.42        35.34        32.32         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       30.81         9.50        14.07        21.04         0.16        18.38 
TCGA-94-A5I4 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
       16.14         5.69        21.21         0.07        76.80        39.85 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3412 TCGA-18-3415 
       65.65        16.80         0.43        75.75        11.34        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       36.07        92.42         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       46.88        99.16        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       31.73       122.43         9.34       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       88.11        41.69        33.93        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1016 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       64.21        27.02        48.33         0.56        38.17        34.75 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5478 
       32.02        19.30         9.57        11.77        63.55         0.79 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
       86.30        71.34        11.74        30.12        56.32        16.64 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
       79.53       103.53       151.27        54.44        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL 
        0.30        36.62         6.94       110.99        44.19        27.16 
TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 
       32.88        81.24        74.66         9.07        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 
       39.32         4.96        38.79         4.04        26.43         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         7.96         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5021 
        6.81         0.39         3.39        21.70       133.25        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        82.52       102.18         1.71        24.33         1.94 
TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       71.18        55.56        40.21        38.66        39.12        33.11 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       13.38        11.77        14.20        13.32        12.16        13.02 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        4.44        10.65        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       28.34         8.75        27.45        28.96        12.43        18.25 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 
       21.90        18.48        14.53        31.27         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 
       17.49        33.24        14.96         4.93        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK 
       20.25        15.81        20.94        19.23        13.32        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26        14.47         0.03        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2697 
       71.24        16.47        85.12        34.36        56.65        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
       10.22        96.82        92.71        21.93        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       56.91        50.33        48.49         3.19        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
       23.57        26.83        11.77        52.67        70.13        70.42 
TCGA-63-7023 TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       55.30        58.65        59.97        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       89.29        78.28        16.37        36.16        53.88        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       16.96        43.10         2.01        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        2.01         0.92         0.99        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
        0.99         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
       19.00         3.02        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       24.95         1.97        25.97        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
        5.03        30.02        10.06         4.01         2.73         6.64 
TCGA-68-7757 TCGA-68-A59I TCGA-70-6723 TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 
        6.94        16.18        12.33        29.56        75.09        23.28 
TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
       11.18        70.13       106.95         0.16        46.78         6.51 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       37.81       156.66        12.59        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 
      104.09        11.54        26.40        27.39         6.97        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-6560 
       60.53        36.36       126.18        22.29        38.86        41.39 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 
       34.95        31.30        32.91         1.38        29.95        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       19.04        24.13        31.56        26.79        30.64        34.52 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 
        0.76        13.22        22.45        16.77         5.29         2.01 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        7.76        36.59        38.14        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       30.28        30.97        19.86        24.36        30.48        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       16.21        15.85        14.96        15.29        29.92        12.39 
TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
       24.92         2.93        20.22         3.48         4.01         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        26.63        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       18.31        17.46        27.68        21.44        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       21.34        27.16        18.15         2.01        27.02        20.32 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       12.89        16.11        11.84         4.54        64.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       57.30        13.74         4.21        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       14.73        26.43        83.57        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.49               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            173.82             156.66 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             27.62              21.07 
[1] "0.5 - 173.8 (27.6)" "0.0 - 156.7 (21.1)"
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         1       17       34        1        18        20
  19P GAIN WILD-TYPE       1       72      118        1        47        75
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  19P GAIN MUTATED           0         19          3        1
  19P GAIN WILD-TYPE         3         44         16        6
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 17                 72
  STAGE IB                 34                118
  STAGE II                  1                  1
  STAGE IIA                18                 47
  STAGE IIB                20                 75
  STAGE III                 0                  3
  STAGE IIIA               19                 44
  STAGE IIIB                3                 16
  STAGE IV                  1                  6
[1] 10  2
[1] 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    20  71  19   5
  19P GAIN WILD-TYPE  92 223  52  19
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               20                 92
  T2               71                223
  T3               19                 52
  T4                5                 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    68  36  10   0
  19P GAIN WILD-TYPE 249  97  30   5
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               68                249
  N1               36                 97
  N2               10                 30
  N3                0                  5
[1] 4 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    97   1
  19P GAIN WILD-TYPE 314   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     97    1
  19P GAIN WILD-TYPE  314    6
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               97                314
  1                1                  6
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    27  88
  19P GAIN WILD-TYPE 103 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     27   88
  19P GAIN WILD-TYPE  103  283
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               27                103
  MALE                 88                283
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    87  17
  19P GAIN WILD-TYPE 297  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     87   17
  19P GAIN WILD-TYPE  297   36
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                87                297
  YES               17                 36
[1] 2 2
[1] FALSE
D34V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED                                       7
  19P GAIN WILD-TYPE                                     8
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  19P GAIN MUTATED                                        1
  19P GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED                                         0
  19P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                           107
  19P GAIN WILD-TYPE                                                         372
D34V10, multiclass
                                                             clus
vv                                                            19P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              107
                                                             clus
vv                                                            19P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                372
[1] 4 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    91   2   1   5
  19P GAIN WILD-TYPE 308  10   3  18
D34V13, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               91                308
  R1                2                 10
  R2                1                  3
  RX                5                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       3                         6    83
  19P GAIN WILD-TYPE     6                        25   266
D34V14, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                6                 25
  WHITE                                   83                266
[1] 3 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     2  70
  19P GAIN WILD-TYPE   6 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   70
  19P GAIN WILD-TYPE    6  247
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               70                247
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    88  72
  19Q GAIN WILD-TYPE 192 142
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               160                334 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                72                142 
$`19Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
        4.47         4.80       133.74        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-A56V TCGA-56-A4BY 
       31.27        17.88        18.38         7.76        12.03        17.85 
TCGA-56-A5DR TCGA-60-2712 TCGA-63-A5MH TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
        0.13         9.01        66.61        57.07        19.36         2.76 
TCGA-J1-A4AH TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 
       19.10        40.90        65.65         0.43         8.58       117.57 
TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 TCGA-21-1071 TCGA-21-1081 
       23.54        36.07        86.96       119.54        46.88         9.34 
TCGA-21-5786 TCGA-21-5787 TCGA-22-1011 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
       33.93        10.82         1.74        20.48        35.08        24.13 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-5477 TCGA-22-5481 TCGA-22-5483 
       38.17        34.75        13.12        44.25        79.20        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-6738 
       30.12        62.86        97.94       173.82       103.53        63.35 
TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
      110.99        44.19         2.63        61.61        32.88        65.23 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 TCGA-34-A5IX TCGA-37-3792 
       60.30        50.66        39.32         1.12        33.90         0.39 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 
        3.39       126.58       111.35        24.33        60.53        36.39 
TCGA-39-5035 TCGA-39-5040 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-A475 
       68.38        17.06        33.11        27.91        22.98         9.73 
TCGA-46-3768 TCGA-52-7809 TCGA-56-6545 TCGA-56-7580 TCGA-56-7582 TCGA-56-8083 
        9.83         5.46        21.90        30.41        19.76         4.93 
TCGA-56-8304 TCGA-56-8629 TCGA-56-A49D TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M 
        3.48        15.81        20.94        34.78        34.36        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2704 TCGA-60-2708 TCGA-60-2719 TCGA-60-2722 
       29.92        21.11        37.94        80.45        42.64        29.85 
TCGA-60-2723 TCGA-63-7020 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5ML 
       35.90        70.13        68.15       102.67        70.62        45.57 
TCGA-63-A5MR TCGA-63-A5MV TCGA-66-2742 TCGA-66-2758 TCGA-66-2763 TCGA-66-2770 
       89.29        36.16        21.07        21.01         0.99        23.01 
TCGA-66-2777 TCGA-66-2782 TCGA-66-2787 TCGA-66-2788 TCGA-66-2793 TCGA-66-2800 
        2.01        12.00        40.01        22.98        10.06        49.05 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 
       13.35        16.18        14.73        12.07        29.56        73.12 
TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7465 TCGA-77-8008 
       11.18         0.49        73.22        70.13        32.55        86.76 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8138 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       55.73       156.66        17.72         6.97        66.51        54.41 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 
      132.36       150.25         5.92        61.94        27.62         9.67 
TCGA-85-7696 TCGA-85-7699 TCGA-85-8350 TCGA-85-8353 TCGA-85-8354 TCGA-85-A4CN 
       36.53        32.91        22.45         3.09        32.71        34.13 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 
       19.73        27.16        15.85        12.39         3.65        11.77 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-A5I6 
       22.62        10.59         2.70         3.48         5.26        17.69 
TCGA-98-8022 TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW 
       30.67         2.01        18.58        20.71        13.18        13.41 
TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-XC-AA0X 
        2.89        14.73         3.65         0.20 

$`19Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19        31.99         6.18        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       14.93        48.82        60.66        64.93        22.06       129.01 
TCGA-33-4589 TCGA-43-2578 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 
        1.55        22.49        78.18         2.93        11.61        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-60-2696 
       13.05         3.45        17.00        16.77        21.04         3.58 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
       41.42        35.34        32.32         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       30.81         9.50        14.07        21.04         0.16        18.38 
TCGA-94-A5I4 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
       16.14         5.69        21.21         0.07        76.80        39.85 
TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3412 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 
       16.80        75.75        11.34        92.15        92.42         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      154.32        49.94        99.16        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       15.58        31.73       122.43       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       88.11        41.69        21.99         7.33         4.31        64.21 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 TCGA-22-4596 TCGA-22-4605 TCGA-22-4607 
       14.10        27.02        48.33         0.56        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 
        9.57        11.77        63.55        14.63         0.79        86.30 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 TCGA-33-4583 
       71.34        11.74        56.32        16.64        79.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       14.07        54.44         4.70         0.30        36.62         6.94 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 
      118.36        27.16        81.24        74.66         9.07        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 
       44.75         4.96        38.79         4.04        26.43         4.01 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         7.96         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 
        0.39        37.58        21.70       133.25        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5036 TCGA-39-5037 
       82.52       102.18         1.71         1.94        71.18        55.56 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       40.21        38.66        39.12        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 
        3.81        19.59        13.38        11.77        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       12.16        13.02         4.44        10.65        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
        0.39        29.95        28.34        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       28.96        12.43        18.25        18.48        14.53        31.27 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8307 
        6.51         0.10        17.49        33.24        14.96        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
        9.93        20.25        19.23        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
       14.47         0.03        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       16.47        85.12        56.65        12.23        10.22        96.82 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       92.71        21.93        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       48.49         3.19        23.57        26.83        11.77        52.67 
TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN 
       70.42        55.30        58.65        59.97        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       25.28        78.28        16.37        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       43.10         2.01         0.99         1.02         2.01         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
        0.99        43.99        25.05         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
        2.01         7.07        19.00         3.02        19.00        12.03 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 
        3.98        24.95         1.97        25.97         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
        5.03        30.02        54.08         4.01         2.73         6.64 
TCGA-68-7757 TCGA-70-6723 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7337 
        6.94        12.33        75.09        23.28       140.09       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
        0.16        46.78         6.51        37.81        12.59        53.92 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8153 
       39.09       104.09        11.54        26.40        27.39        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-6560 
       60.53        36.36       126.18        22.29        38.86        41.39 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 
       40.24         6.41        34.95        31.30         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       29.95        18.94        25.15        19.04        24.13        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       26.79        30.64        34.52        10.09         0.76        13.22 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
       16.77         5.29         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB 
       38.14        12.59        18.08        22.59        30.28        30.97 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
       19.86        24.36        30.48        16.21        14.96        15.29 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 
       29.92        24.92         2.93        20.22         4.01         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        4.01         5.03        26.63        14.14        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 
       17.46        27.68        21.44        30.81        21.34        27.16 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 
       18.15        27.02        20.32        12.89        16.11        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        64.54         1.22        57.30        13.74         4.21 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N 
       49.28        43.92        25.32        26.43        83.57        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
        3.72        12.72        43.89        11.18 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.13               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            173.82             154.32 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            25.745             20.285 
[1] "0.1 - 173.8 (25.7)" "0.0 - 154.3 (20.3)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         1       25       47        1        24        28
  19Q GAIN WILD-TYPE       1       64      105        1        41        67
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  19Q GAIN MUTATED           0         27          6        3
  19Q GAIN WILD-TYPE         3         36         13        4
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 25                 64
  STAGE IB                 47                105
  STAGE II                  1                  1
  STAGE IIA                24                 41
  STAGE IIB                28                 67
  STAGE III                 0                  3
  STAGE IIIA               27                 36
  STAGE IIIB                6                 13
  STAGE IV                  3                  4
[1] 10  2
[1] 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    31 102  20  10
  19Q GAIN WILD-TYPE  81 192  51  14
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               31                 81
  T2              102                192
  T3               20                 51
  T4               10                 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
  19Q GAIN MUTATED    99  47  17   0
  19Q GAIN WILD-TYPE 218  86  23   5
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               99                218
  N1               47                 86
  N2               17                 23
  N3                0                  5
[1] 4 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   135   3
  19Q GAIN WILD-TYPE 276   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    135    3
  19Q GAIN WILD-TYPE  276    4
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0              135                276
  1                3                  4
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    41 122
  19Q GAIN WILD-TYPE  89 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     41  122
  19Q GAIN WILD-TYPE   89  249
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               41                 89
  MALE                122                249
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   129  18
  19Q GAIN WILD-TYPE 255  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    129   18
  19Q GAIN WILD-TYPE  255   35
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO               129                255
  YES               18                 35
[1] 2 2
[1] FALSE
D35V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                       8
  19Q GAIN WILD-TYPE                                     7
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  19Q GAIN MUTATED                                        0
  19Q GAIN WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                         0
  19Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                           155
  19Q GAIN WILD-TYPE                                                         324
D35V10, multiclass
                                                             clus
vv                                                            19Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              155
                                                             clus
vv                                                            19Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D35V11, continuous
D35V12, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED   131   3   0   8
  19Q GAIN WILD-TYPE 268   9   4  15
D35V13, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0              131                268
  R1                3                  9
  R2                0                  4
  RX                8                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       5                        13   108
  19Q GAIN WILD-TYPE     4                        18   241
D35V14, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    5                  4
  BLACK OR AFRICAN AMERICAN               13                 18
  WHITE                                  108                241
[1] 3 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     3  96
  19Q GAIN WILD-TYPE   5 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   96
  19Q GAIN WILD-TYPE    5  221
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               96                221
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   141 118
  20P GAIN WILD-TYPE 139  96
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               259                235 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               118                 96 
$`20P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-21-A5DI TCGA-22-5471 TCGA-22-5472 
        4.47       123.19         4.80        32.19        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 
       22.06       129.01         1.55        28.96        17.88        22.49 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 
        7.76        78.18         2.93        11.61        12.03        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2711 
        3.45        17.00        16.77        21.04         0.13        41.42 
TCGA-60-2715 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-94-7557 
       35.34         8.02        20.78        42.08        30.81         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
       18.38        16.14        57.07        19.36         2.76         5.69 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
       19.10         0.07        40.90        16.80         0.43         8.58 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-5592 
      117.57        11.34        23.54        92.15        36.07        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 
      119.54        46.88        60.89        34.78       122.43         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-22-1011 
      119.80        43.23        88.11        41.69        33.93         1.74 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4604 TCGA-22-4605 
       27.02        20.48        48.33        24.13        13.12        32.02 
TCGA-22-4609 TCGA-22-5477 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        9.57        44.25        71.34        11.74        18.84        30.12 
TCGA-22-5491 TCGA-33-4538 TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-33-AASD 
       56.32        97.94       103.53        54.44        63.35       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
       44.19       118.36         2.63        61.61        32.88        65.23 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 
       60.30        50.66        39.32         1.12         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-4130 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
       33.90         4.01         8.12         0.39         3.39        37.58 
TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 
       21.70       126.58       111.35        68.58         1.71        24.33 
TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-3920 TCGA-43-5670 
       60.53        71.18        55.56        40.21        33.11        27.91 
TCGA-43-6143 TCGA-43-6773 TCGA-43-7656 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 
       22.98         3.81        19.59        13.02         9.83        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 
       13.91         0.39        29.95        28.34         5.46         8.75 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       28.96        18.25        21.90        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8622 TCGA-56-8624 
       30.41        19.76         6.51        17.49         1.81        13.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8391 
       20.94        19.23        18.74        14.47         0.03        71.24 
TCGA-58-8393 TCGA-58-A46K TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       34.78        34.36        21.11        10.22        96.82        37.94 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       21.93        80.45        42.64         3.19        29.85        35.90 
TCGA-60-2726 TCGA-63-7020 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML 
       11.77        70.13       102.67        70.62        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2737 TCGA-66-2742 
       14.99        78.28        36.16        53.88         2.01        21.07 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2769 TCGA-66-2770 
        0.99        21.01        25.05         0.99         7.07        23.01 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        3.02         2.01        12.03         3.98        12.00        24.95 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 
       40.01        22.98        30.02        10.06        49.05         6.64 
TCGA-68-8251 TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6844 
       13.35        16.18        12.07        12.33        29.56        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       23.28        11.18       140.09         0.49        73.22         0.16 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        6.51        86.76        55.73       156.66        53.92        39.09 
TCGA-77-8143 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GF 
       26.40        36.36       150.25        22.29        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 
       38.86         9.67        40.24        36.53        31.30         1.15 
TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 
       29.95        19.04        24.13        31.56        34.52        10.09 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8353 TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 
        0.76        22.45         3.09         7.76        18.08        22.59 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A510 
       34.13        30.97        19.86        30.48        27.16        15.85 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
       12.39         3.65         2.93        11.77        20.22        22.62 
TCGA-92-7341 TCGA-92-8064 TCGA-94-A5I6 TCGA-98-8021 TCGA-98-8022 TCGA-98-A53B 
        3.48         5.26        17.69        30.81        30.67         2.01 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       18.58        20.71        12.89        16.11        13.18        13.41 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54         1.22        57.30        13.74         4.21         2.89 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q 
       25.32        14.73        83.57         3.65        33.07         3.72 
TCGA-O2-A52S 
       12.72 

$`20P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 
       12.20        31.99         6.18        27.19        14.93        48.82 
TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 TCGA-43-5668 TCGA-56-7221 
      133.74        19.76        31.50        31.27        18.38        19.99 
TCGA-56-A4BY TCGA-60-2696 TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH TCGA-90-7766 
       17.85         3.58         9.01        32.32        66.61         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-98-A53D TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT 
       14.07        21.04        21.21        76.80        39.85        65.65 
TCGA-18-3408 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1072 
       75.75        92.42        86.96         2.79       154.32        99.16 
TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 TCGA-21-5782 TCGA-21-5787 TCGA-22-0940 
       70.16        15.58        31.73        31.63        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-4593 TCGA-22-4596 
        7.33         4.31        64.21        14.10        35.08         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       38.17        34.75        19.30        11.77        63.55        14.63 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 TCGA-33-4547 
        0.79        86.30        79.20        62.86        16.64        79.53 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      173.82       151.27        14.07         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASL TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 
        6.94        27.16        81.24        74.66         9.07        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       44.75         4.96        38.79         0.43         0.39         7.96 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 
        7.46         7.82         6.81       133.25        55.20        82.52 
TCGA-39-5027 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 
      102.18         1.94        36.39        68.38        17.06        38.66 
TCGA-43-3394 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-8116 
       39.12        24.89        21.47         5.46        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3769 TCGA-51-4080 
        9.73        14.20        13.32        12.16         4.44         0.39 
TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 
       30.35        27.45        12.43         0.10        33.24        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 
        4.93         3.48        26.89        14.07         1.35        22.75 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A5DS 
       10.36         9.93        20.25        15.81        13.32         0.26 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L 
       13.25        13.55        29.95        16.47        85.12        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 
       35.24        29.92        12.23        92.71        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 
       56.91        50.33        48.49        23.57        26.83        52.67 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MI TCGA-63-A5MN TCGA-63-A5MP 
       70.42        68.15        55.30        58.65        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2744 
       89.29        16.37        34.59        16.96        43.10         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 
        1.02         2.01         0.92        43.99         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2785 TCGA-66-2786 
        2.01         2.01        19.00        19.00         1.97        25.97 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 
        4.04        22.98         5.03        54.08         4.01         2.73 
TCGA-68-7757 TCGA-68-A59J TCGA-77-6843 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
        6.94        14.73        73.12        70.13       106.95        46.78 
TCGA-77-7465 TCGA-77-8128 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       32.55        37.81        12.59        17.72       104.09        11.54 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       27.39         6.97        66.51        54.41        65.49        60.53 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 
      126.18       132.36         5.92        41.39         6.41        34.95 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 
       32.91         1.38        18.94        25.15        26.79        30.64 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       13.22        16.77         5.29        32.71         2.01        15.39 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR 
       36.59        38.14        12.59        30.28        24.36        19.73 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-A59Q 
       16.21        14.96        15.29        29.92        24.92        10.59 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        2.70         4.01         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       14.14        71.01        18.31        17.46        27.68        21.44 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-MF-A522 
       21.34        27.16        18.15        27.02        20.32        11.84 
TCGA-NC-A5HG TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HT TCGA-O2-A52V TCGA-O2-A5IB 
       64.54        49.28        43.92        26.43        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.03               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            156.66             173.82 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             22.29              21.21 
[1] "0.0 - 156.7 (22.3)" "0.1 - 173.8 (21.2)"
[1] "hr=" "1.1"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         2       40       83        1        31        55
  20P GAIN WILD-TYPE       0       49       69        1        34        40
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  20P GAIN MUTATED           2         33          9        6
  20P GAIN WILD-TYPE         1         30         10        1
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 40                 49
  STAGE IB                 83                 69
  STAGE II                  1                  1
  STAGE IIA                31                 34
  STAGE IIB                55                 40
  STAGE III                 2                  1
  STAGE IIIA               33                 30
  STAGE IIIB                9                 10
  STAGE IV                  6                  1
[1] 10  2
[1] 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    47 163  39  14
  20P GAIN WILD-TYPE  65 131  32  10
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               47                 65
  T2              163                131
  T3               39                 32
  T4               14                 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
  20P GAIN MUTATED   166  70  22   1
  20P GAIN WILD-TYPE 151  63  18   4
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              166                151
  N1               70                 63
  N2               22                 18
  N3                1                  4
[1] 4 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   217   6
  20P GAIN WILD-TYPE 194   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    217    6
  20P GAIN WILD-TYPE  194    1
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              217                194
  1                6                  1
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    54 209
  20P GAIN WILD-TYPE  76 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     54  209
  20P GAIN WILD-TYPE   76  162
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               54                 76
  MALE                209                162
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   201  33
  20P GAIN WILD-TYPE 183  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    201   33
  20P GAIN WILD-TYPE  183   20
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               201                183
  YES               33                 20
[1] 2 2
[1] FALSE
D36V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                      10
  20P GAIN WILD-TYPE                                     5
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  20P GAIN MUTATED                                        2
  20P GAIN WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                         1
  20P GAIN WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                           250
  20P GAIN WILD-TYPE                                                         229
D36V10, multiclass
                                                             clus
vv                                                            20P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              250
                                                             clus
vv                                                            20P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                229
[1] 4 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   207   6   3  13
  20P GAIN WILD-TYPE 192   6   1  10
D36V13, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              207                192
  R1                6                  6
  R2                3                  1
  RX               13                 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                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       6                        16   183
  20P GAIN WILD-TYPE     3                        15   166
D36V14, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    6                  3
  BLACK OR AFRICAN AMERICAN               16                 15
  WHITE                                  183                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     7 163
  20P GAIN WILD-TYPE   1 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7  163
  20P GAIN WILD-TYPE    1  154
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                  1
  NOT HISPANIC OR LATINO              163                154
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   138 109
  20Q GAIN WILD-TYPE 142 105
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               247                247 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               109                105 
$`20Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-21-A5DI TCGA-22-5472 TCGA-22-A5C4 
        4.47       123.19         4.80        32.19        64.93        22.06 
TCGA-33-4532 TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 
      129.01         1.55        31.50        28.96        31.27        17.88 
TCGA-43-2578 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 
       22.49        78.18         2.93        12.03        13.05         3.45 
TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2711 TCGA-60-2715 TCGA-68-8250 
       16.77        21.04         0.13        41.42        35.34         8.02 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
       20.78        42.08        30.81         0.16        18.38        16.14 
TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM 
       57.07         2.76         5.69        19.10         0.07        39.85 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3412 TCGA-18-3414 
       40.90        16.80         0.43         8.58        11.34        23.54 
TCGA-18-3417 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 
       36.07        49.94       119.54        46.88        60.89        34.78 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5784 TCGA-21-5786 
       31.73         9.34       119.80        43.23        41.69        33.93 
TCGA-21-5787 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       10.82         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4605 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 
       48.33        24.13        32.02        71.34        18.84        30.12 
TCGA-22-5491 TCGA-33-4538 TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-33-AASD 
       56.32        97.94       103.53        54.44        63.35       110.99 
TCGA-33-AASI TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 
       44.19         2.63        32.88        65.23        60.30        50.66 
TCGA-34-5928 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 
       39.32         4.04        26.43        33.90         4.01         0.39 
TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN 
        8.12         6.81         0.39         3.39        37.58        21.70 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 
      133.25       126.58       111.35         1.71        24.33        60.53 
TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       71.18        55.56        40.21        33.11        27.91        22.98 
TCGA-43-7656 TCGA-46-3767 TCGA-46-3768 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 
       19.59        13.02         9.83        13.91         5.46        30.35 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 
        8.75        28.96        18.25        21.90        18.48        14.53 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7822 TCGA-56-8082 TCGA-56-8624 TCGA-56-8626 
       31.27        19.76        17.49        14.96        13.81         9.93 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8393 
       20.94        19.23        18.74        14.47         0.03        34.78 
TCGA-58-A46K TCGA-60-2695 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       34.36        21.11        96.82        92.71        21.93        80.45 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2726 TCGA-63-7020 
       50.33        42.64         3.19        29.85        11.77        70.13 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MS 
      102.67        70.62        59.97        45.57        14.99        78.28 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 
       36.16        53.88         2.01        21.07         0.99         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2769 TCGA-66-2770 
       43.99        21.01        25.05         0.99         7.07        23.01 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 
        2.01        12.03         3.98        12.00         1.97        40.01 
TCGA-66-2788 TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I 
       22.98        10.06        49.05         6.64        13.35        16.18 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       12.07        12.33        23.28        11.18       140.09         0.49 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
      106.95         0.16        46.78        32.55         6.51        86.76 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
      156.66        53.92        39.09        26.40         6.97        66.51 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
      150.25        22.29         5.92        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 
       41.39        40.24        36.53         1.15        29.95        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
       24.13        31.56        34.52        10.09         0.76        22.45 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 
       16.77         3.09        32.71         7.76        38.14        18.08 
TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       22.59        30.97        19.86        30.48        19.73        27.16 
TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
       15.85        12.39         3.65         2.93        11.77        20.22 
TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-98-8022 
       22.62         3.48         5.26        14.14        17.69        30.67 
TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A446 
       27.16         2.01        18.58        20.71        12.89        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       13.41        11.84         4.54        64.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       13.74        25.32        14.73        83.57         3.65        33.07 
TCGA-O2-A52S 
       12.72 

$`20Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 
       12.20        31.99         6.18        27.19        14.93        48.82 
TCGA-22-5471 TCGA-33-4533 TCGA-33-6737 TCGA-43-5668 TCGA-43-7657 TCGA-43-A474 
       60.66       133.74        19.76        18.38         7.76        11.61 
TCGA-56-7221 TCGA-56-8308 TCGA-56-A4BY TCGA-60-2696 TCGA-60-2712 TCGA-60-2721 
       19.99        17.00        17.85         3.58         9.01        32.32 
TCGA-63-A5MH TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-96-A4JK TCGA-98-A53D 
       66.61         9.50        14.07        21.04        19.36        21.21 
TCGA-NC-A5HE TCGA-NK-A5CT TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3419 
       76.80        65.65        75.75       117.57        92.15        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 
       86.96         2.79       154.32        99.16        70.16        15.58 
TCGA-21-1080 TCGA-21-5782 TCGA-21-5783 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
      122.43        31.63        88.11        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 
       64.21         0.56        38.17        34.75        13.12        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 TCGA-22-5492 TCGA-33-4547 
       86.30        79.20        11.74        62.86        16.64        79.53 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      173.82       151.27        14.07         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-5232 TCGA-34-5234 
        6.94       118.36        27.16        61.61        81.24        74.66 
TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
        9.07        16.93        44.75         4.96         1.12        38.79 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-39-5021 TCGA-39-5022 
        0.43         7.96         7.46         7.82        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 
       82.52       102.18         1.94        36.39        68.38        17.06 
TCGA-43-2581 TCGA-43-3394 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       38.66        39.12        24.89        21.47         5.46         3.81 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        4.44        10.65         0.39         0.39        29.95        28.34 
TCGA-52-7812 TCGA-56-5897 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 
       27.45        12.43        30.41         6.51         0.10        33.24 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        4.93         3.48        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A5DS 
       22.75        10.36        20.25        15.81        13.32         0.26 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J 
       13.25        13.55        29.95        71.24        16.47        85.12 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 
       56.65        35.24        29.92        12.23        10.22        37.94 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2723 TCGA-60-2724 
       49.48        66.54        56.91        48.49        35.90        23.57 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MI 
       26.83        52.67        70.42        68.15        55.30        58.65 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2727 
       11.34        25.28        89.29        16.37        34.59        16.96 
TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2765 TCGA-66-2766 
       43.10         1.02         2.01         0.92         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2783 
        2.01         2.01        19.00         3.02        19.00        24.95 
TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
       25.97         4.04        22.98         5.03        30.02        54.08 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
        4.01         2.73         6.94        14.73        29.56        73.12 
TCGA-77-6844 TCGA-77-7142 TCGA-77-7335 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 
       75.09        73.22        70.13        55.73        37.81        12.59 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 
       17.72       104.09        11.54        27.39        54.41        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 TCGA-85-6798 
       60.53        36.36       126.18       132.36        61.94         6.41 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 
       34.95        31.30        32.91         1.38        18.94        25.15 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 
       26.79        30.64        13.22         5.29         2.01        15.39 
TCGA-85-8580 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A50Z 
       36.59        12.59        30.28        34.13        24.36        16.21 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-A59Q TCGA-92-7340 
       14.96        15.29        29.92        24.92        10.59         2.70 
TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 
        4.01         2.30         4.01         5.03        26.63        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 
       18.31        17.46        27.68        21.44        30.81        21.34 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-L3-A524 TCGA-NC-A5HK TCGA-NC-A5HL 
       18.15        27.02        20.32        16.11         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HT TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB 
       49.28        43.92        26.43         3.72        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.03               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            156.66             173.82 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             22.06              21.34 
[1] "0.0 - 156.7 (22.1)" "0.1 - 173.8 (21.3)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         2       40       78        0        32        48
  20Q GAIN WILD-TYPE       0       49       74        2        33        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  20Q GAIN MUTATED           1         34          9        6
  20Q GAIN WILD-TYPE         2         29         10        1
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 40                 49
  STAGE IB                 78                 74
  STAGE II                  0                  2
  STAGE IIA                32                 33
  STAGE IIB                48                 47
  STAGE III                 1                  2
  STAGE IIIA               34                 29
  STAGE IIIB                9                 10
  STAGE IV                  6                  1
[1] 10  2
[1] 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    48 151  37  15
  20Q GAIN WILD-TYPE  64 143  34   9
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               48                 64
  T2              151                143
  T3               37                 34
  T4               15                  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
  20Q GAIN MUTATED   159  66  22   0
  20Q GAIN WILD-TYPE 158  67  18   5
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              159                158
  N1               66                 67
  N2               22                 18
  N3                0                  5
[1] 4 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   207   6
  20Q GAIN WILD-TYPE 204   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    207    6
  20Q GAIN WILD-TYPE  204    1
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              207                204
  1                6                  1
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    49 202
  20Q GAIN WILD-TYPE  81 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     49  202
  20Q GAIN WILD-TYPE   81  169
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               49                 81
  MALE                202                169
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   190  30
  20Q GAIN WILD-TYPE 194  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    190   30
  20Q GAIN WILD-TYPE  194   23
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               190                194
  YES               30                 23
[1] 2 2
[1] FALSE
D37V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                      11
  20Q GAIN WILD-TYPE                                     4
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  20Q GAIN MUTATED                                        2
  20Q GAIN WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                         1
  20Q GAIN WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                           237
  20Q GAIN WILD-TYPE                                                         242
D37V10, multiclass
                                                             clus
vv                                                            20Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              237
                                                             clus
vv                                                            20Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D37V11, continuous
D37V12, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   198   5   1  12
  20Q GAIN WILD-TYPE 201   7   3  11
D37V13, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              198                201
  R1                5                  7
  R2                1                  3
  RX               12                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       6                        16   174
  20Q GAIN WILD-TYPE     3                        15   175
D37V14, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    6                  3
  BLACK OR AFRICAN AMERICAN               16                 15
  WHITE                                  174                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     6 160
  20Q GAIN WILD-TYPE   2 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6  160
  20Q GAIN WILD-TYPE    2  157
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO              160                157
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    35  21
  21Q GAIN WILD-TYPE 245 193
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                56                438 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                193 
$`21Q GAIN MUTATED`
TCGA-18-3410 TCGA-21-A5DI TCGA-22-A5C4 TCGA-34-2605 TCGA-56-7221 TCGA-56-8201 
        4.80        32.19        22.06        28.96        19.99        13.05 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-63-A5MH TCGA-77-A5GA TCGA-96-7545 
       17.00        16.77        17.85        66.61        42.08        57.07 
TCGA-NC-A5HR TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-22-1011 TCGA-22-4595 
       40.90        34.78         9.34       119.80         1.74        24.13 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-34-2596 TCGA-34-5240 TCGA-34-5928 
      173.82       151.27        54.44         2.63        50.66        39.32 
TCGA-39-5028 TCGA-43-6143 TCGA-43-6647 TCGA-43-A475 TCGA-60-2706 TCGA-60-2714 
        1.71        22.98        24.89         9.73        92.71        50.33 
TCGA-60-2724 TCGA-63-A5MG TCGA-63-A5MR TCGA-66-2756 TCGA-66-2767 TCGA-66-2770 
       23.57        70.62        89.29         0.99         2.01        23.01 
TCGA-66-2783 TCGA-70-6722 TCGA-77-6844 TCGA-77-7139 TCGA-77-8130 TCGA-77-8139 
       24.95        12.07        75.09       140.09       156.66       104.09 
TCGA-77-8143 TCGA-77-A5G7 TCGA-85-6560 TCGA-85-7844 TCGA-85-7950 TCGA-85-8277 
       26.40         5.92        41.39        29.95        18.94        10.09 
TCGA-85-8353 TCGA-85-A4JB TCGA-92-7340 TCGA-LA-A7SW TCGA-NC-A5HG TCGA-NC-A5HI 
        3.09        30.97         2.70        13.41        64.54        57.30 
TCGA-NC-A5HT TCGA-O2-A5IB 
       26.43        11.18 

$`21Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19        31.99         6.18        27.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 
       14.93        48.82        60.66        64.93       129.01       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 
        1.55        19.76        31.50        31.27        17.88        22.49 
TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       18.38         7.76        78.18         2.93        11.61        12.03 
TCGA-56-8305 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
        3.45        21.04         0.13         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 
       35.34        32.32         8.02        20.78        30.81         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK 
       14.07        21.04         0.16        18.38        16.14        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE 
        2.76         5.69        21.21        19.10         0.07        76.80 
TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       39.85        65.65        16.80         0.43         8.58        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
      117.57        11.34        23.54        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       86.96         2.79       154.32        49.94       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       99.16        70.16        60.89        15.58        31.73       122.43 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
       43.23        31.63        88.11        41.69        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 
       21.99         7.33         4.31        64.21        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       20.48        35.08        48.33         0.56        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       13.12        32.02        19.30         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       14.63        44.25         0.79        86.30        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       11.74        18.84        30.12        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN 
       97.94        79.53       103.53        14.07        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        0.30        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       27.16        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
        9.07        60.30        16.93        44.75         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       38.79         4.04        26.43        33.90         4.01         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.39         7.96         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 
        0.39         3.39        37.58        21.70       133.25       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 
      111.35        68.58        55.20        82.52       102.18        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        60.53        36.39        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       17.06        40.21        38.66        39.12        33.11        27.91 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       21.47         5.46         3.81        19.59        13.38        11.77 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       14.20        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       10.65        13.91         0.39         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        5.46        30.35         8.75        27.45        28.96        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       18.25        21.90        18.48        14.53        31.27        30.41 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       19.76         6.51         0.10        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        4.93         3.48        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       20.94        19.23        13.32        18.74         0.26        14.47 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.03        13.25        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       34.78        85.12        34.36        56.65        35.24        29.92 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 
       21.11        12.23        10.22        96.82        37.94        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2719 
       80.45        49.48        66.54        56.91        48.49        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
        3.19        29.85        35.90        26.83        11.77        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI 
       70.13        70.42        68.15        55.30       102.67        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS 
       59.97        45.57        14.99        11.34        25.28        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       16.37        36.16        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
        2.01        21.07         0.99         1.02         2.01         0.92 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
       43.99        21.01        25.05         0.99         2.01         1.02 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01         7.07        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
       12.03         3.98        12.00         1.97        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
       22.98         4.04        22.98         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       54.08         4.01        49.05         2.73         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 
       13.35        16.18        14.73        12.33        29.56        73.12 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       23.28        11.18         0.49        73.22        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        0.16        46.78        32.55         6.51        86.76        55.73 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 
       37.81        12.59        53.92        39.09        17.72        11.54 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       27.39         6.97        66.51        54.41        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 
       36.36       126.18       132.36       150.25        22.29        61.94 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86         9.67        40.24         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 
       34.95        31.30        32.91         1.38         1.15        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       19.04        24.13        31.56        26.79        30.64        34.52 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
        0.76        13.22        22.45        16.77         5.29        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01        15.39         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA 
       18.08        22.59        30.28        34.13        19.86        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       30.48        19.73        27.16        16.21        15.85        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 
       15.29        29.92        12.39         3.65        24.92         2.93 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
       11.77        20.22        22.62        10.59         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        5.26         2.30         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       17.69        71.01        18.31        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B 
       30.81        30.67        21.34        27.16        18.15         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 
       27.02        20.32        18.58        20.71        12.89        16.11 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
       13.18        11.84         4.54         1.22        13.74         4.21 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR 
        2.89        49.28        43.92        25.32        14.73        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
        3.65        33.07         3.72        12.72        43.89         0.20 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.99               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            173.82             154.32 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            25.675             21.055 
[1] "1.0 - 173.8 (25.7)" "0.0 - 154.3 (21.1)"
[1] "hr=" "1.6"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         0        6       16        0         4        15
  21Q GAIN WILD-TYPE       2       83      136        2        61        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  21Q GAIN MUTATED           1         11          4        0
  21Q GAIN WILD-TYPE         2         52         15        7
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  6                 83
  STAGE IB                 16                136
  STAGE II                  0                  2
  STAGE IIA                 4                 61
  STAGE IIB                15                 80
  STAGE III                 1                  2
  STAGE IIIA               11                 52
  STAGE IIIB                4                 15
  STAGE IV                  0                  7
[1] 10  2
[1] 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     7  32  15   3
  21Q GAIN WILD-TYPE 105 262  56  21
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                7                105
  T2               32                262
  T3               15                 56
  T4                3                 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                  N0  N1  N2  N3
  21Q GAIN MUTATED    30  22   3   2
  21Q GAIN WILD-TYPE 287 111  37   3
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               30                287
  N1               22                111
  N2                3                 37
  N3                2                  3
[1] 4 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    46   0
  21Q GAIN WILD-TYPE 365   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     46    0
  21Q GAIN WILD-TYPE  365    7
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               46                365
  1                0                  7
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    11  46
  21Q GAIN WILD-TYPE 119 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     11   46
  21Q GAIN WILD-TYPE  119  325
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               11                119
  MALE                 46                325
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    41  12
  21Q GAIN WILD-TYPE 343  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     41   12
  21Q GAIN WILD-TYPE  343   41
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                41                343
  YES               12                 41
[1] 2 2
[1] FALSE
D38V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                       4
  21Q GAIN WILD-TYPE                                    11
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  21Q GAIN MUTATED                                        0
  21Q GAIN WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                         1
  21Q GAIN WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                            52
  21Q GAIN WILD-TYPE                                                         427
D38V10, multiclass
                                                             clus
vv                                                            21Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               52
                                                             clus
vv                                                            21Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                427
[1] 4 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    43   3   1   5
  21Q GAIN WILD-TYPE 356   9   3  18
D38V13, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               43                356
  R1                3                  9
  R2                1                  3
  RX                5                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       1                         1    41
  21Q GAIN WILD-TYPE     8                        30   308
D38V14, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                1                 30
  WHITE                                   41                308
[1] 3 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  35
  21Q GAIN WILD-TYPE   8 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   35
  21Q GAIN WILD-TYPE    8  282
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               35                282
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED   131  87
  22Q GAIN WILD-TYPE 149 127
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               218                276 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                87                127 
$`22Q GAIN MUTATED`
TCGA-18-3409 TCGA-33-4532 TCGA-33-4589 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 
      123.19       129.01         1.55        28.96        31.27        17.88 
TCGA-43-5668 TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       18.38         7.76         2.93        11.61        12.03        19.99 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2711 
        3.45        17.00        16.77        21.04         0.13        41.42 
TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-94-7033 TCGA-94-7943 
       66.61        20.78        42.08        30.81        21.04        18.38 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH 
       16.14        57.07        19.36         2.76         5.69        19.10 
TCGA-NC-A5HD TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-21-1072 
        0.07        75.75       117.57        11.34        23.54        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 
       70.16        60.89        34.78        31.73       119.80        43.23 
TCGA-21-5784 TCGA-21-5786 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 
       41.69        33.93         4.31         1.74        14.10        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-5477 
       35.08        24.13        34.75        13.12        32.02        44.25 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 TCGA-33-4586 
       86.30        79.20        11.74        56.32        16.64        14.07 
TCGA-33-6738 TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
       63.35       110.99       118.36         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-8455 
       65.23         9.07        60.30        50.66        16.93         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-4130 TCGA-37-4133 TCGA-37-4141 TCGA-37-A5EN 
       26.43        33.90         8.12         7.82         0.39        21.70 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 
      111.35        68.58        36.39        71.18        55.56        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-A475 
       33.11        27.91        22.98        24.89        21.47         9.73 
TCGA-46-3766 TCGA-46-3768 TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
       12.16         9.83        10.65         5.46        30.35         8.75 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 
       28.96        12.43        18.25        21.90        31.27        30.41 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8083 
       19.76         6.51         0.10        17.49        33.24         4.93 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
        1.35         1.81         9.93        15.81        20.94        19.23 
TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-A46M 
       13.32         0.26         0.03        13.25        29.95        35.24 
TCGA-58-A46N TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       29.92        96.82        37.94        92.71        21.93        80.45 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       50.33        42.64         3.19        29.85        35.90        26.83 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       11.77        70.13        55.30       102.67        70.62        58.65 
TCGA-63-A5ML TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2734 
       45.57        78.28        16.37        36.16        53.88        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 
        2.01        21.07         0.92        21.01         0.99         7.07 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
        3.02         2.01         3.98        24.95         1.97        22.98 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 
       30.02        54.08        49.05        14.73        29.56        23.28 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 
      140.09         0.49         0.16        46.78         6.51        86.76 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8140 TCGA-77-8143 
       37.81       156.66        12.59        53.92        11.54        26.40 
TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GF 
        6.97        65.49        36.36       132.36         5.92        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 TCGA-85-8052 
       38.86         9.67        40.24        36.53        31.30        24.13 
TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8354 TCGA-85-8481 
       31.56        34.52        10.09        22.45        32.71         7.76 
TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
       36.59        34.13        30.97        19.86        30.48        19.73 
TCGA-85-A50M TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-92-7341 TCGA-94-A4VJ 
       27.16         3.65         2.93        11.77         3.48        14.14 
TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53J 
       17.69        18.31        17.46        30.67        27.16        20.71 
TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NK-A5CR 
       13.18        64.54        57.30        49.28        25.32        83.57 
TCGA-O2-A52N TCGA-XC-AA0X 
       33.07         0.20 

$`22Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 TCGA-43-2578 TCGA-43-7658 TCGA-56-8201 
      133.74        19.76        31.50        22.49        78.18        13.05 
TCGA-56-A4BY TCGA-60-2696 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 
       17.85         3.58         9.01        35.34        32.32         8.02 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7557 TCGA-98-A53D TCGA-NC-A5HE TCGA-NC-A5HM 
        9.50        14.07         0.16        21.21        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3415 
       40.90        65.65        16.80         0.43         8.58        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       36.07        92.42        86.96         2.79       154.32        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 
      119.54        46.88        15.58       122.43         9.34        31.63 
TCGA-21-5783 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1016 
       88.11        10.82        21.99         7.33        64.21        27.02 
TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       48.33         0.56        38.17        19.30         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 
       63.55        14.63         0.79        71.34        18.84        30.12 
TCGA-22-5489 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       62.86        97.94        79.53       173.82       103.53       151.27 
TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI 
       54.44         4.70         0.30        36.62         6.94        44.19 
TCGA-33-AASL TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       27.16        81.24        74.66        44.75        39.32         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
        1.12        38.79         4.01         0.43         0.39         7.96 
TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 
        7.46         6.81         3.39        37.58       133.25       126.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        82.52       102.18         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-6771 
       60.53        68.38        17.06        40.21        38.66         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 
        3.81        19.59        13.38        11.77        14.20        13.32 
TCGA-46-3767 TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       13.02         4.44        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7812 TCGA-56-7222 TCGA-56-7223 TCGA-56-8082 TCGA-56-8304 
       28.34        27.45        18.48        14.53        14.96         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 
       26.89        14.07        22.75        13.81        10.36        20.25 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       18.74        14.47        13.55        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 
       85.12        34.36        56.65        21.11        12.23        10.22 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2724 TCGA-63-6202 
       49.48        66.54        56.91        48.49        23.57        52.67 
TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       70.42        68.15        59.97        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MY TCGA-66-2727 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       89.29        34.59        16.96         0.99         1.02         2.01 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
        0.99        43.99        25.05         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
        2.01        23.01        19.00        19.00        12.03        12.00 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 
       25.97        40.01         4.04        22.98         5.03        10.06 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
        4.01         2.73         6.64         6.94        13.35        16.18 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7142 
       12.07        12.33        73.12        75.09        11.18        73.22 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 TCGA-77-8009 TCGA-77-8136 TCGA-77-8138 
       70.13       106.95        32.55        55.73        39.09        17.72 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ 
      104.09        27.39        66.51        54.41        60.53       126.18 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 
      150.25        22.29        61.94        41.39         6.41        34.95 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       32.91         1.38         1.15        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
       19.04        26.79        30.64         0.76        13.22        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8582 TCGA-85-8584 
        5.29         3.09         2.01        15.39        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A510 
       18.08        22.59        30.28        24.36        16.21        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED 
       14.96        15.29        29.92        12.39        24.92        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       22.62        10.59         2.70         4.01         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-A4JL TCGA-98-7454 
        4.01         5.03        26.63        71.01        27.68        21.44 
TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       30.81        21.34        18.15         2.01        27.02        20.32 
TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       18.58        12.89        16.11        13.41        11.84         4.54 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HQ 
        1.22        13.74         4.21         2.89        43.92        14.73 
TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       26.43         3.65         3.72        12.72        43.89        11.18 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.03               0.16 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            156.66             173.82 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            24.510             19.445 
[1] "0.0 - 156.7 (24.5)" "0.2 - 173.8 (19.4)"
[1] "hr=" "1.2"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         1       33       80        0        28        46
  22Q GAIN WILD-TYPE       1       56       72        2        37        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  22Q GAIN MUTATED           0         22          7        5
  22Q GAIN WILD-TYPE         3         41         12        2
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 33                 56
  STAGE IB                 80                 72
  STAGE II                  0                  2
  STAGE IIA                28                 37
  STAGE IIB                46                 49
  STAGE III                 0                  3
  STAGE IIIA               22                 41
  STAGE IIIB                7                 12
  STAGE IV                  5                  2
[1] 10  2
[1] 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    42 143  26  11
  22Q GAIN WILD-TYPE  70 151  45  13
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               42                 70
  T2              143                151
  T3               26                 45
  T4               11                 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
  22Q GAIN MUTATED   148  53  15   1
  22Q GAIN WILD-TYPE 169  80  25   4
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0              148                169
  N1               53                 80
  N2               15                 25
  N3                1                  4
[1] 4 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   187   5
  22Q GAIN WILD-TYPE 224   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED    187    5
  22Q GAIN WILD-TYPE  224    2
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0              187                224
  1                5                  2
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    50 172
  22Q GAIN WILD-TYPE  80 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     50  172
  22Q GAIN WILD-TYPE   80  199
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               50                 80
  MALE                172                199
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED   176  19
  22Q GAIN WILD-TYPE 208  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED    176   19
  22Q GAIN WILD-TYPE  208   34
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO               176                208
  YES               19                 34
[1] 2 2
[1] FALSE
D39V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                       6
  22Q GAIN WILD-TYPE                                     9
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  22Q GAIN MUTATED                                        1
  22Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                         0
  22Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                           215
  22Q GAIN WILD-TYPE                                                         264
D39V10, multiclass
                                                             clus
vv                                                            22Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              215
                                                             clus
vv                                                            22Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                264
[1] 4 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   182   6   1   7
  22Q GAIN WILD-TYPE 217   6   3  16
D39V13, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0              182                217
  R1                6                  6
  R2                1                  3
  RX                7                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       2                         9   157
  22Q GAIN WILD-TYPE     7                        22   192
D39V14, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                9                 22
  WHITE                                  157                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3 139
  22Q GAIN WILD-TYPE   5 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3  139
  22Q GAIN WILD-TYPE    5  178
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO              139                178
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    39  24
  XP GAIN WILD-TYPE 241 190
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               63               431 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               24               190 
$`XP GAIN MUTATED`
TCGA-18-3406 TCGA-18-4083 TCGA-33-4532 TCGA-43-7657 TCGA-43-7658 TCGA-56-8504 
       12.20         6.18       129.01         7.76        78.18        16.77 
TCGA-77-7140 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK TCGA-J1-A4AH TCGA-NK-A7XE 
       20.78         0.16        16.14        19.36        19.10         0.43 
TCGA-18-3421 TCGA-21-1081 TCGA-21-5786 TCGA-22-4593 TCGA-22-4595 TCGA-33-4587 
       86.96         9.34        33.93        35.08        24.13        54.44 
TCGA-33-A4WN TCGA-33-AASI TCGA-34-2596 TCGA-34-5240 TCGA-34-5928 TCGA-37-5819 
        4.70        44.19         2.63        50.66        39.32         3.39 
TCGA-39-5019 TCGA-39-5036 TCGA-43-3920 TCGA-43-5670 TCGA-43-A475 TCGA-56-7223 
      111.35        71.18        33.11        27.91         9.73        14.53 
TCGA-56-7730 TCGA-56-8307 TCGA-56-A4BW TCGA-58-8386 TCGA-58-A46M TCGA-58-A46N 
        6.51        26.89        19.23         0.03        35.24        29.92 
TCGA-60-2695 TCGA-60-2703 TCGA-60-2719 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5ML 
       21.11        96.82        42.64        23.57        11.77        45.57 
TCGA-63-A5MW TCGA-66-2756 TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 TCGA-66-2793 
       53.88         0.99        21.01         1.02         7.07        10.06 
TCGA-77-7138 TCGA-77-7335 TCGA-77-8136 TCGA-77-8153 TCGA-85-7710 TCGA-85-8070 
       11.18        70.13        39.09        65.49         1.38        31.56 
TCGA-85-8072 TCGA-85-8350 TCGA-92-7341 TCGA-94-A4VJ TCGA-98-8022 TCGA-98-A538 
       30.64        22.45         3.48        14.14        30.67        27.16 
TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HN 
        1.22         4.21        49.28 

$`XP GAIN WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI 
        4.47       123.19         4.80        31.99        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 
       14.93        48.82        60.66        64.93        22.06       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 
        1.55        19.76        31.50        28.96        31.27        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       22.49        18.38         2.93        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
       13.05         3.45        17.00        17.85        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
        3.58        41.42         9.01        35.34        32.32        66.61 
TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
        8.02        42.08        30.81         9.50        14.07        21.04 
TCGA-94-7943 TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD 
       18.38        57.07         2.76         5.69        21.21         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W 
       76.80        39.85        40.90        65.65        16.80         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
       75.75       117.57        11.34        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       92.42         2.79       154.32        49.94       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       99.16        70.16        60.89        34.78        15.58        31.73 
TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
      122.43       119.80        43.23        31.63        88.11        41.69 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       10.82        21.99         7.33         4.31        64.21         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       14.10        27.02        20.48        48.33         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       34.75        13.12        32.02        19.30         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       63.55        14.63        44.25         0.79        86.30        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       16.64        97.94        79.53       173.82       103.53       151.27 
TCGA-33-4586 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       14.07        63.35         0.30        36.62         6.94       110.99 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
      118.36        27.16        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
       74.66         9.07        60.30        16.93        44.75         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        38.79         4.04        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         7.96         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 
        6.81         0.39        37.58        21.70       133.25       126.58 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 
        1.94        60.53        36.39        68.38        55.56        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       40.21        38.66        39.12        22.98        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U 
        5.46         3.81        19.59        13.38        11.77        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
       13.32        12.16        13.02         9.83         4.44        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       13.91         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       30.35         8.75        27.45        28.96        12.43        18.25 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 
       21.90        18.48        31.27        30.41        19.76         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 
       17.49        33.24        14.96         4.93         3.48        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
       20.25        15.81        20.94        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
       14.47        13.25        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2697 TCGA-60-2698 
       34.78        85.12        34.36        56.65        12.23        10.22 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       56.91        50.33        48.49         3.19        29.85        35.90 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       26.83        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN 
      102.67        70.62        58.65        59.97        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MY 
       25.28        89.29        78.28        16.37        36.16        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       16.96        43.10         2.01        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        2.01         0.92        43.99        25.05         0.99         2.01 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         2.01        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       25.97        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       30.02        54.08         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 
        6.94        13.35        16.18        14.73        12.07        12.33 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
       29.56        73.12        75.09        23.28       140.09         0.49 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       73.22       106.95         0.16        46.78        32.55         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       86.76        55.73        37.81       156.66        12.59        53.92 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       17.72       104.09        11.54        26.40        27.39         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       66.51        54.41        60.53        36.36       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH 
      150.25        22.29         5.92        61.94        27.62        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
        9.67        41.39        40.24         6.41        36.53        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       31.30        32.91         1.15        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       19.04        24.13        26.79        34.52        10.09         0.76 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       13.22        16.77         5.29         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
       15.39         7.76        36.59        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
       22.59        30.28        34.13        30.97        19.86        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       30.48        19.73        27.16        16.21        15.85        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 
       15.29        29.92        12.39         3.65        24.92         2.93 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
       11.77        20.22        22.62        10.59         2.70         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 
        5.26         2.30         4.01         5.03        26.63        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       71.01        18.31        17.46        27.68        21.44        30.81 
TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       21.34        18.15         2.01        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HO 
        4.54        64.54        57.30        13.74         2.89        43.92 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       25.32        14.73        26.43        83.57         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        12.72        43.89        11.18         0.20 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.03              0.07 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           129.01            173.82 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            21.11             21.90 
[1] "0.0 - 129.0 (21.1)" "0.1 - 173.8 (21.9)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         0        9       20        0         9        15
  XP GAIN WILD-TYPE       2       80      132        2        56        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  XP GAIN MUTATED           0          5          5        1
  XP GAIN WILD-TYPE         3         58         14        6
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 9                80
  STAGE IB                20               132
  STAGE II                 0                 2
  STAGE IIA                9                56
  STAGE IIB               15                80
  STAGE III                0                 3
  STAGE IIIA               5                58
  STAGE IIIB               5                14
  STAGE IV                 1                 6
[1] 10  2
[1] 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    10  41   8   5
  XP GAIN WILD-TYPE 102 253  63  19
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              10               102
  T2              41               253
  T3               8                63
  T4               5                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
  XP GAIN MUTATED    39  19   5   0
  XP GAIN WILD-TYPE 278 114  35   5
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              39               278
  N1              19               114
  N2               5                35
  N3               0                 5
[1] 4 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    53   1
  XP GAIN WILD-TYPE 358   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     53    1
  XP GAIN WILD-TYPE  358    6
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              53               358
  1               1                 6
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    17  47
  XP GAIN WILD-TYPE 113 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     17   47
  XP GAIN WILD-TYPE  113  324
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              17               113
  MALE                47               324
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    53   5
  XP GAIN WILD-TYPE 331  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     53    5
  XP GAIN WILD-TYPE  331   48
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               53               331
  YES               5                48
[1] 2 2
[1] FALSE
D40V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  XP GAIN MUTATED                                       4
  XP GAIN WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  XP GAIN MUTATED                                        0
  XP GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  XP GAIN MUTATED                                         1
  XP GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XP GAIN MUTATED                                                            59
  XP GAIN WILD-TYPE                                                         420
D40V10, multiclass
                                                             clus
vv                                                            XP GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              59
                                                             clus
vv                                                            XP GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               420
[1] 4 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    50   3   0   2
  XP GAIN WILD-TYPE 349   9   4  21
D40V13, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              50               349
  R1               3                 9
  R2               0                 4
  RX               2                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         3    49
  XP GAIN WILD-TYPE     9                        28   300
D40V14, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               3                28
  WHITE                                  49               300
[1] 3 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  43
  XP GAIN WILD-TYPE   8 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   43
  XP GAIN WILD-TYPE    8  274
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              43               274
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    46  31
  XQ GAIN WILD-TYPE 234 183
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               77               417 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               31               183 
$`XQ GAIN MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-4083 TCGA-33-4532 TCGA-43-7657 TCGA-56-8504 
       12.20         4.47         6.18       129.01         7.76        16.77 
TCGA-60-2711 TCGA-77-7140 TCGA-77-A5GA TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK 
       41.42        20.78        42.08         0.16        16.14        19.36 
TCGA-J1-A4AH TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 
       19.10         0.43        75.75        11.34        36.07        86.96 
TCGA-21-1081 TCGA-22-1012 TCGA-22-4593 TCGA-22-4595 TCGA-22-5483 TCGA-33-4566 
        9.34        14.10        35.08        24.13        18.84       173.82 
TCGA-33-AASJ TCGA-34-2596 TCGA-34-5240 TCGA-34-5928 TCGA-34-8454 TCGA-34-8456 
      118.36         2.63        50.66        39.32        38.79        26.43 
TCGA-37-4133 TCGA-37-5819 TCGA-39-5019 TCGA-43-3920 TCGA-43-5670 TCGA-43-A475 
        7.82         3.39       111.35        33.11        27.91         9.73 
TCGA-51-4079 TCGA-56-7223 TCGA-56-7730 TCGA-56-8624 TCGA-56-8629 TCGA-56-A4BW 
        0.39        14.53         6.51        13.81        15.81        19.23 
TCGA-58-8386 TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2703 TCGA-60-2719 
        0.03        35.24        29.92        21.11        96.82        42.64 
TCGA-60-2724 TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MT TCGA-66-2756 TCGA-66-2758 
       23.57        45.57        25.28        16.37         0.99        21.01 
TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 TCGA-66-2781 TCGA-66-2793 TCGA-70-6723 
        1.02         7.07         3.02         3.98        10.06        12.33 
TCGA-77-6842 TCGA-77-7138 TCGA-77-7335 TCGA-77-8009 TCGA-77-A5GF TCGA-85-6561 
       29.56        11.18        70.13        55.73        27.62        40.24 
TCGA-85-7710 TCGA-85-8070 TCGA-85-8072 TCGA-85-8350 TCGA-85-8354 TCGA-85-A50M 
        1.38        31.56        30.64        22.45        32.71        27.16 
TCGA-92-7341 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-98-A538 TCGA-NC-A5HN 
        3.48        14.14        17.69        27.16        49.28 

$`XQ GAIN WILD-TYPE`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
      123.19         4.80        31.99        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 
       48.82        60.66        64.93        22.06       133.74         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 
       19.76        31.50        28.96        31.27        17.88        22.49 
TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       18.38        78.18         2.93        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
       13.05         3.45        17.00        17.85        21.04         0.13 
TCGA-60-2696 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 
        3.58         9.01        35.34        32.32        66.61         8.02 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 
       30.81         9.50        14.07        21.04        18.38        57.07 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        2.76         5.69        21.21         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3411 TCGA-18-3414 
       40.90        65.65        16.80         8.58       117.57        23.54 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.15        92.42         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       46.88        99.16        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       31.73       122.43       119.80        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       41.69        33.93        10.82        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 
       64.21         1.74        27.02        20.48        48.33         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       38.17        34.75        13.12        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       11.77        63.55        14.63        44.25         0.79        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       71.34        79.20        11.74        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       16.64        97.94        79.53       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       54.44        63.35         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
      110.99        44.19        27.16        61.61        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 
       81.24        74.66         9.07        60.30        16.93        44.75 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        4.96         1.12         4.04        33.90         4.01         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 
        0.39         7.96         8.12         7.46         6.81         0.39 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 
       37.58        21.70       133.25       126.58        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       36.39        68.38        71.18        55.56        17.06        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       38.66        39.12        22.98        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 
        3.81        19.59        13.38        11.77        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       12.16        13.02         9.83         4.44        10.65        13.91 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
        0.39        29.95        28.34         5.46        30.35         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
       27.45        28.96        12.43        18.25        21.90        18.48 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       31.27        30.41        19.76         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       14.96         4.93         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D 
        1.81        22.75        10.36         9.93        20.25        20.94 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 
       13.32        18.74         0.26        14.47        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       56.65        12.23        10.22        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       80.45        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
        3.19        29.85        35.90        26.83        11.77        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG 
       70.13        70.42        68.15        55.30       102.67        70.62 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS 
       58.65        59.97        14.99        11.34        89.29        78.28 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
       36.16        53.88        34.59        16.96        43.10         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
       21.07         0.99         1.02         2.01         0.92        43.99 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
       25.05         0.99         2.01         2.01         2.01        23.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
       19.00         2.01        19.00        12.03        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1.97        25.97        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
        5.03        30.02        54.08         4.01        49.05         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        6.64         6.94        13.35        16.18        14.73        12.07 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       73.12        75.09        23.28       140.09         0.49        73.22 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
      106.95         0.16        46.78        32.55         6.51        86.76 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       37.81       156.66        12.59        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
      104.09        11.54        26.40        27.39         6.97        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       54.41        65.49        60.53        36.36       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 
      150.25        22.29         5.92        61.94        38.86         9.67 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       41.39         6.41        36.53        34.95        31.30        32.91 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1.15        29.95        18.94        25.15        19.04        24.13 
TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
       26.79        34.52        10.09         0.76        13.22        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        5.29         3.09         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       38.14        12.59        18.08        22.59        30.28        34.13 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z 
       30.97        19.86        24.36        30.48        19.73        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       15.85        14.96        15.29        29.92        12.39         3.65 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       24.92         2.93        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
        2.70         4.01         5.26         2.30         4.01         5.03 
TCGA-94-8491 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       26.63        71.01        18.31        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.81        30.67        21.34        18.15         2.01        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       20.32        18.58        20.71        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       13.41        11.84         4.54        64.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       13.74         4.21         2.89        43.92        25.32        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       26.43        83.57         3.65        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.03              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           173.82            156.66 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            20.78             21.99 
[1] "0.0 - 173.8 (20.8)" "0.1 - 156.7 (22.0)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         0        6       27        0        14        18
  XQ GAIN WILD-TYPE       2       83      125        2        51        77
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  XQ GAIN MUTATED           0          7          5        2
  XQ GAIN WILD-TYPE         3         56         14        5
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 6                83
  STAGE IB                27               125
  STAGE II                 0                 2
  STAGE IIA               14                51
  STAGE IIB               18                77
  STAGE III                0                 3
  STAGE IIIA               7                56
  STAGE IIIB               5                14
  STAGE IV                 2                 5
[1] 10  2
[1] 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     8  54  11   6
  XQ GAIN WILD-TYPE 104 240  60  18
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               8               104
  T2              54               240
  T3              11                60
  T4               6                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ GAIN MUTATED    47  25   5   0
  XQ GAIN WILD-TYPE 270 108  35   5
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              47               270
  N1              25               108
  N2               5                35
  N3               0                 5
[1] 4 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    66   2
  XQ GAIN WILD-TYPE 345   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     66    2
  XQ GAIN WILD-TYPE  345    5
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              66               345
  1               2                 5
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    17  62
  XQ GAIN WILD-TYPE 113 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     17   62
  XQ GAIN WILD-TYPE  113  309
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              17               113
  MALE                62               309
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    61   7
  XQ GAIN WILD-TYPE 323  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     61    7
  XQ GAIN WILD-TYPE  323   46
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               61               323
  YES               7                46
[1] 2 2
[1] FALSE
D41V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED                                       3
  XQ GAIN WILD-TYPE                                    12
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  XQ GAIN MUTATED                                        1
  XQ GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED                                         0
  XQ GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                            75
  XQ GAIN WILD-TYPE                                                         404
D41V10, multiclass
                                                             clus
vv                                                            XQ GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              75
                                                             clus
vv                                                            XQ GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               404
[1] 4 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    64   3   0   4
  XQ GAIN WILD-TYPE 335   9   4  19
D41V13, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              64               335
  R1               3                 9
  R2               0                 4
  RX               4                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       3                         4    54
  XQ GAIN WILD-TYPE     6                        27   295
D41V14, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               4                27
  WHITE                                  54               295
[1] 3 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   8 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   54
  XQ GAIN WILD-TYPE    8  263
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              54               263
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    82  70
  1P LOSS WILD-TYPE 198 144
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              152               342 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               70               144 
$`1P LOSS MUTATED`
TCGA-18-3406 TCGA-22-1017 TCGA-22-5471 TCGA-34-2605 TCGA-43-7657 TCGA-43-A474 
       12.20        48.82        60.66        28.96         7.76        11.61 
TCGA-43-A56V TCGA-56-8305 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       12.03         3.45        18.38        16.14        57.07        19.36 
TCGA-98-A539 TCGA-NC-A5HE TCGA-NC-A5HR TCGA-18-3408 TCGA-18-5592 TCGA-21-1071 
        5.69        76.80        40.90        75.75        49.94        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 
       99.16        70.16        34.78        33.93        21.99         7.33 
TCGA-22-1012 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
       14.10        35.08        24.13         0.56        38.17        13.12 
TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5491 
        9.57        63.55        14.63        44.25        86.30        56.32 
TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       97.94       151.27        14.07         0.30        36.62         6.94 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-8456 TCGA-37-4129 
       44.19        27.16         2.63        61.61        26.43         7.96 
TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5027 TCGA-39-5029 
        3.39        37.58        21.70       126.58       102.18        24.33 
TCGA-39-5034 TCGA-43-2581 TCGA-43-3394 TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 
       36.39        38.66        39.12         9.83        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 
        0.39        29.95        28.34         8.75        28.96        18.25 
TCGA-56-6545 TCGA-56-7580 TCGA-56-7730 TCGA-56-7822 TCGA-56-7823 TCGA-56-A49D 
       21.90        30.41         6.51        17.49        33.24        20.94 
TCGA-56-A4BX TCGA-56-A62T TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M 
       13.32        14.47        16.47        34.78        56.65        35.24 
TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2714 TCGA-63-7023 TCGA-63-A5MB 
       10.22        92.71        21.93        50.33        55.30       102.67 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-66-2737 TCGA-66-2758 
       59.97        45.57        25.28        89.29         2.01        21.01 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 
        2.01        23.01         3.02         2.01         3.98        40.01 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J TCGA-70-6723 TCGA-77-7139 TCGA-77-7141 
        2.73         6.94        14.73        12.33       140.09         0.49 
TCGA-77-7337 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 
      106.95        32.55        55.73        37.81        53.92        66.51 
TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 
       54.41       150.25        27.62         9.67        40.24        36.53 
TCGA-85-7698 TCGA-85-7843 TCGA-85-8049 TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 
       31.30         1.15        19.04        10.09         0.76         5.29 
TCGA-85-8353 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A511 TCGA-85-A53L 
        3.09        36.59        30.28        34.13        14.96        12.39 
TCGA-85-A5B5 TCGA-90-A4EE TCGA-92-7341 TCGA-94-8490 TCGA-96-7544 TCGA-98-8021 
        3.65        22.62         3.48         5.03        71.01        30.81 
TCGA-98-8023 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
       21.34        18.58        20.71        16.11        13.18        11.84 
TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-O2-A52N 
        2.89        43.92        25.32        14.73        83.57        33.07 
TCGA-O2-A52S TCGA-O2-A52V 
       12.72        43.89 

$`1P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
        4.47       123.19         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       32.19        14.93        64.93        22.06       129.01       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 
        1.55        19.76        31.50        31.27        17.88        22.49 
TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 
       18.38        78.18         2.93        19.99        13.05        17.00 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       16.77        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
        9.01        35.34        32.32        66.61         8.02        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       42.08        30.81         9.50        14.07        21.04         0.16 
TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NK-A5CT 
        2.76        21.21        19.10         0.07        39.85        65.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       16.80         0.43         8.58       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       92.15        36.07        92.42        86.96         2.79       154.32 
TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
      119.54        60.89        15.58        31.73       122.43         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 
      119.80        43.23        31.63        88.11        41.69        10.82 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
        4.31        64.21         1.74        27.02        20.48        48.33 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 
       34.75        32.02        19.30        11.77         0.79        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 
       79.20        11.74        18.84        30.12        62.86        16.64 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
       79.53       173.82       103.53        54.44        63.35         4.70 
TCGA-33-AASD TCGA-33-AASJ TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
      110.99       118.36        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        60.30        50.66        16.93        44.75        39.32 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 
        4.96         1.12        38.79         4.04        33.90         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         0.39         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        0.39       133.25       111.35        68.58        55.20        82.52 
TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.71         1.94        60.53        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       17.06        40.21        33.11        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       21.47         5.46         3.81        19.59        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 
        9.73        14.20        13.32        12.16        13.02         4.44 
TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-7222 
       10.65         5.46        30.35        27.45        12.43        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-8082 TCGA-56-8083 
       14.53        31.27        19.76         0.10        14.96         4.93 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        3.48        26.89        14.07         1.35         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
       13.81        10.36         9.93        20.25        15.81        19.23 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       18.74         0.26         0.03        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       71.24        85.12        34.36        29.92        21.11        12.23 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       96.82        37.94        80.45        49.48        66.54        56.91 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       48.49        42.64         3.19        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       26.83        11.77        52.67        70.13        70.42        68.15 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT 
       70.62        58.65        14.99        11.34        78.28        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
       36.16        53.88        34.59        16.96        43.10        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        0.99         1.02         2.01         0.92         0.99        43.99 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
       25.05         0.99         2.01         1.02         2.01         7.07 
TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        19.00        12.03        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-68-7756 TCGA-68-8251 
       25.97        22.98         4.04        22.98         6.64        13.35 
TCGA-68-A59I TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       16.18        12.07        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
       11.18        73.22        70.13         0.16        46.78         6.51 
TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       86.76       156.66        12.59        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 TCGA-77-8154 
       11.54        26.40        27.39         6.97        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       36.36       126.18       132.36        22.29         5.92        61.94 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
       38.86        41.39         6.41        34.95        32.91         1.38 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       29.95        18.94        25.15        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 
       30.64        34.52        13.22        22.45        16.77        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        2.01        15.39         7.76        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       22.59        30.97        19.86        24.36        30.48        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 
       27.16        16.21        15.85        15.29        29.92        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
        2.93        11.77        20.22        10.59         2.70         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        5.26         2.30         4.01        26.63        14.14        17.69 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-A538 
       18.31        17.46        27.68        21.44        30.67        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A7SW 
       18.15         2.01        27.02        20.32        12.89        13.41 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        64.54         1.22        57.30        13.74         4.21 
TCGA-NC-A5HN TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A5IB TCGA-XC-AA0X 
       49.28        26.43         3.65         3.72        11.18         0.20 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.30              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           151.27            173.82 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            24.23             21.04 
[1] "0.3 - 151.3 (24.2)" "0.0 - 173.8 (21.0)"
[1] "hr=" "1.1"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         1       25       41        1        25        30
  1P LOSS WILD-TYPE       1       64      111        1        40        65
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  1P LOSS MUTATED           1         20          9        1
  1P LOSS WILD-TYPE         2         43         10        6
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                25                64
  STAGE IB                41               111
  STAGE II                 1                 1
  STAGE IIA               25                40
  STAGE IIB               30                65
  STAGE III                1                 2
  STAGE IIIA              20                43
  STAGE IIIB               9                10
  STAGE IV                 1                 6
[1] 10  2
[1] 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    33  92  22   8
  1P LOSS WILD-TYPE  79 202  49  16
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              33                79
  T2              92               202
  T3              22                49
  T4               8                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
  1P LOSS MUTATED    84  54  13   2
  1P LOSS WILD-TYPE 233  79  27   3
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              84               233
  N1              54                79
  N2              13                27
  N3               2                 3
[1] 4 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   128   1
  1P LOSS WILD-TYPE 283   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    128    1
  1P LOSS WILD-TYPE  283    6
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0             128               283
  1               1                 6
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    32 123
  1P LOSS WILD-TYPE  98 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     32  123
  1P LOSS WILD-TYPE   98  248
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              32                98
  MALE               123               248
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED   115  21
  1P LOSS WILD-TYPE 269  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    115   21
  1P LOSS WILD-TYPE  269   32
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO              115               269
  YES              21                32
[1] 2 2
[1] FALSE
D42V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED                                       4
  1P LOSS WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  1P LOSS MUTATED                                        1
  1P LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED                                         0
  1P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                           150
  1P LOSS WILD-TYPE                                                         329
D42V10, multiclass
                                                             clus
vv                                                            1P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             150
                                                             clus
vv                                                            1P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D42V11, continuous
D42V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED   125   3   2   7
  1P LOSS WILD-TYPE 274   9   2  16
D42V13, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0             125               274
  R1               3                 9
  R2               2                 2
  RX               7                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       2                        11   109
  1P LOSS WILD-TYPE     7                        20   240
D42V14, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN              11                20
  WHITE                                 109               240
[1] 3 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     5  93
  1P LOSS WILD-TYPE   3 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5   93
  1P LOSS WILD-TYPE    3  224
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO              93               224
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    29  30
  1Q LOSS WILD-TYPE 251 184
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               59               435 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               30               184 
$`1Q LOSS MUTATED`
TCGA-22-5471 TCGA-34-2605 TCGA-43-A474 TCGA-43-A56V TCGA-96-7545 TCGA-96-A4JK 
       60.66        28.96        11.61        12.03        57.07        19.36 
TCGA-98-A539 TCGA-21-5786 TCGA-22-4593 TCGA-22-4595 TCGA-22-4604 TCGA-22-5477 
        5.69        33.93        35.08        24.13        13.12        44.25 
TCGA-22-5491 TCGA-33-A5GW TCGA-33-AASB TCGA-37-4129 TCGA-37-A5EL TCGA-39-5029 
       56.32         0.30         6.94         7.96        37.58        24.33 
TCGA-39-5034 TCGA-43-3394 TCGA-46-6026 TCGA-51-4079 TCGA-52-7811 TCGA-56-5898 
       36.39        39.12        13.91         0.39         8.75        18.25 
TCGA-56-6545 TCGA-56-7580 TCGA-56-7730 TCGA-56-7822 TCGA-56-A49D TCGA-56-A62T 
       21.90        30.41         6.51        17.49        20.94        14.47 
TCGA-58-8392 TCGA-60-2714 TCGA-60-2719 TCGA-63-6202 TCGA-63-A5MB TCGA-63-A5MP 
       16.47        50.33        42.64        52.67       102.67        25.28 
TCGA-63-A5MR TCGA-66-2791 TCGA-66-2793 TCGA-68-7755 TCGA-70-6723 TCGA-77-8128 
       89.29         5.03        10.06         2.73        12.33        37.81 
TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G3 TCGA-85-6175 TCGA-85-7843 
       53.92        66.51        54.41       150.25         9.67         1.15 
TCGA-85-8287 TCGA-85-A4CN TCGA-85-A53L TCGA-96-7544 TCGA-98-8021 TCGA-98-8023 
        0.76        34.13        12.39        71.01        30.81        21.34 
TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52S 
        2.89        14.73        83.57        33.07        12.72 

$`1Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-22-A5C4 
       27.19        32.19        14.93        48.82        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 
      129.01       133.74         1.55        19.76        31.50        31.27 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       17.88        22.49        18.38         7.76        78.18         2.93 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY 
       19.99        13.05         3.45        17.00        16.77        17.85 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       21.04         0.13         3.58        41.42         9.01        35.34 
TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       32.32        66.61         8.02        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        9.50        14.07        21.04         0.16        18.38        16.14 
TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        2.76        21.21        19.10         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       40.90        65.65        16.80         0.43         8.58        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
      117.57        11.34        23.54        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       86.96         2.79       154.32        49.94       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       99.16        70.16        60.89        34.78        15.58        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
      122.43         9.34       119.80        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       41.69        10.82        21.99         7.33         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 
        1.74        14.10        27.02        20.48        48.33         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       38.17        34.75        32.02        19.30         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       63.55        14.63         0.79        86.30        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 
       11.74        18.84        30.12        62.86        16.64        97.94 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       79.53       173.82       103.53       151.27        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
       63.35         4.70        36.62       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       39.32         4.96         1.12        38.79         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 
       33.90         4.01         0.43         0.39         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 
        7.82         6.81         0.39         3.39        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.71         1.94        60.53        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       17.06        40.21        38.66        33.11        27.91        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       11.77         9.73        14.20        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        9.83         4.44        10.65         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-7222 
        5.46        30.35        27.45        28.96        12.43        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 
       14.53        31.27        19.76         0.10        33.24        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        4.93         3.48        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 
       19.23        13.32        18.74         0.26         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       13.55        29.95        71.24        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 
       56.65        35.24        29.92        21.11        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       96.82        37.94        92.71        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       66.54        56.91        48.49         3.19        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       23.57        26.83        11.77        70.13        70.42        68.15 
TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
       55.30        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       11.34        78.28        16.37        36.16        53.88        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       16.96        43.10         2.01        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        2.01         0.92         0.99        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
        0.99         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
       23.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        3.98        12.00        24.95         1.97        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
       22.98         4.04        22.98        30.02        54.08         4.01 
TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       49.05         6.64         6.94        13.35        16.18        14.73 
TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.07        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 
       46.78        32.55         6.51        86.76        55.73       156.66 
TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       12.59        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       27.39         6.97        65.49        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH 
      132.36        22.29         5.92        61.94        27.62        38.86 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       41.39        40.24         6.41        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       32.91         1.38        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       24.13        31.56        26.79        30.64        34.52        10.09 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       13.22        22.45        16.77         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01        15.39         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
       18.08        22.59        30.28        30.97        19.86        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       30.48        19.73        27.16        16.21        15.85        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
       15.29        29.92         3.65        24.92         2.93        11.77 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       20.22        22.62        10.59         2.70         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        5.26         2.30         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 
       17.69        18.31        17.46        27.68        21.44        30.67 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       27.16        18.15         2.01        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        64.54         1.22        57.30        13.74         4.21 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52Q 
       49.28        43.92        25.32        26.43         3.65         3.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.30              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           150.25            173.82 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             21.9              21.7 
[1] "0.3 - 150.2 (21.9)" "0.0 - 173.8 (21.7)"
[1] "hr=" "1.3"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         1        7       13        0        14        11
  1Q LOSS WILD-TYPE       1       82      139        2        51        84
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  1Q LOSS MUTATED           1         10          3        0
  1Q LOSS WILD-TYPE         2         53         16        7
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 7                82
  STAGE IB                13               139
  STAGE II                 0                 2
  STAGE IIA               14                51
  STAGE IIB               11                84
  STAGE III                1                 2
  STAGE IIIA              10                53
  STAGE IIIB               3                16
  STAGE IV                 0                 7
[1] 10  2
[1] 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    12  34  11   3
  1Q LOSS WILD-TYPE 100 260  60  21
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              12               100
  T2              34               260
  T3              11                60
  T4               3                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                 N0  N1  N2  N3
  1Q LOSS MUTATED    33  19   7   1
  1Q LOSS WILD-TYPE 284 114  33   4
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              33               284
  N1              19               114
  N2               7                33
  N3               1                 4
[1] 4 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    49   0
  1Q LOSS WILD-TYPE 362   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     49    0
  1Q LOSS WILD-TYPE  362    7
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              49               362
  1               0                 7
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    12  48
  1Q LOSS WILD-TYPE 118 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     12   48
  1Q LOSS WILD-TYPE  118  323
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              12               118
  MALE                48               323
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    44  11
  1Q LOSS WILD-TYPE 340  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     44   11
  1Q LOSS WILD-TYPE  340   42
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               44               340
  YES              11                42
[1] 2 2
[1] FALSE
D43V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED                                       0
  1Q LOSS WILD-TYPE                                    15
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  1Q LOSS MUTATED                                        1
  1Q LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED                                         0
  1Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                            59
  1Q LOSS WILD-TYPE                                                         420
D43V10, multiclass
                                                             clus
vv                                                            1Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              59
                                                             clus
vv                                                            1Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      15
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               420
[1] 4 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    46   3   2   1
  1Q LOSS WILD-TYPE 353   9   2  22
D43V13, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              46               353
  R1               3                 9
  R2               2                 2
  RX               1                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       2                         6    39
  1Q LOSS WILD-TYPE     7                        25   310
D43V14, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               6                25
  WHITE                                  39               310
[1] 3 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  36
  1Q LOSS WILD-TYPE   6 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   36
  1Q LOSS WILD-TYPE    6  281
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              36               281
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    16   8
  2P LOSS WILD-TYPE 264 206
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               470 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               206 
$`2P LOSS MUTATED`
TCGA-33-4533 TCGA-43-2578 TCGA-NC-A5HM TCGA-NC-A5HR TCGA-18-3421 TCGA-21-1082 
      133.74        22.49        39.85        40.90        86.96       119.80 
TCGA-21-5787 TCGA-22-4594 TCGA-22-5481 TCGA-37-4141 TCGA-37-5819 TCGA-39-5028 
       10.82        48.33        79.20         0.39         3.39         1.71 
TCGA-39-5029 TCGA-51-4081 TCGA-56-1622 TCGA-56-7823 TCGA-56-8307 TCGA-66-2756 
       24.33        29.95        28.96        33.24        26.89         0.99 
TCGA-66-2763 TCGA-68-A59J TCGA-77-7465 TCGA-85-8352 TCGA-92-8064 TCGA-NK-A5CR 
        0.99        14.73        32.55         5.29         5.26        83.57 

$`2P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 
       27.19        32.19        14.93        48.82        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
       22.06       129.01         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       31.27        17.88        18.38         7.76        78.18         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 
       11.61        12.03        19.99        13.05         3.45        17.00 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       16.77        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
        9.01        35.34        32.32        66.61         8.02        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       42.08        30.81         9.50        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
       18.38        16.14        57.07        19.36         2.76         5.69 
TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 
       21.21        19.10         0.07        76.80        65.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        0.43         8.58        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       92.15        36.07        92.42         2.79       154.32        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      119.54        46.88        99.16        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 
       15.58        31.73       122.43         9.34        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       88.11        41.69        33.93        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       64.21         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       24.13         0.56        38.17        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       19.30         9.57        11.77        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        0.79        86.30        71.34        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        56.32        16.64        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        0.30        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       39.32         4.96         1.12        38.79         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       33.90         4.01         0.43         0.39         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        7.46         7.82         6.81        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        60.53        36.39        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       17.06        40.21        38.66        39.12        33.11        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       22.98        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       13.02         9.83         4.44        10.65        13.91         0.39 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
        0.39        28.34         5.46        30.35         8.75        27.45 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       12.43        18.25        21.90        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 
       30.41        19.76         6.51         0.10        17.49        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        4.93         3.48        14.07         1.35         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
       13.81        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       19.23        13.32        18.74         0.26        14.47         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.25        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       85.12        34.36        56.65        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       12.23        10.22        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       80.45        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       11.34        25.28        89.29        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       53.88        34.59        16.96        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
        0.99         1.02         2.01         0.92        43.99        21.01 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       25.05         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
       23.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        3.98        12.00        24.95         1.97        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
       22.98         4.04        22.98         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       54.08         4.01        49.05         2.73         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 
       13.35        16.18        12.07        12.33        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       75.09        23.28        11.18       140.09         0.49        73.22 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 
       70.13       106.95         0.16        46.78         6.51        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       55.73        37.81       156.66        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       17.72       104.09        11.54        26.40        27.39         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       66.51        54.41        65.49        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      132.36       150.25        22.29         5.92        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       38.86         9.67        41.39        40.24         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       34.95        31.30        32.91         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       18.94        25.15        19.04        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       30.64        34.52        10.09         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         3.09        32.71         2.01        15.39         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       36.59        38.14        12.59        18.08        22.59        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       34.13        30.97        19.86        24.36        30.48        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       27.16        16.21        15.85        14.96        15.29        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
       12.39         3.65        24.92         2.93        11.77        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
       22.62        10.59         2.70         3.48         4.01         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        26.63        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       18.31        17.46        27.68        21.44        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       21.34        27.16        18.15         2.01        27.02        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       18.58        20.71        12.89        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       11.84         4.54        64.54         1.22        57.30        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.21         2.89        49.28        43.92        25.32        14.73 
TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       26.43         3.65        33.07         3.72        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.39              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           133.74            173.82 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           27.925            21.390 
[1] "0.4 - 133.7 (27.9)" "0.0 - 173.8 (21.4)"
[1] "hr=" "1.5"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        2        8        0         3         3
  2P LOSS WILD-TYPE       2       87      144        2        62        92
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  2P LOSS MUTATED           0          6          1        0
  2P LOSS WILD-TYPE         3         57         18        7
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                87
  STAGE IB                 8               144
  STAGE II                 0                 2
  STAGE IIA                3                62
  STAGE IIB                3                92
  STAGE III                0                 3
  STAGE IIIA               6                57
  STAGE IIIB               1                18
  STAGE IV                 0                 7
[1] 10  2
[1] 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     4  15   3   2
  2P LOSS WILD-TYPE 108 279  68  22
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               4               108
  T2              15               279
  T3               3                68
  T4               2                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                 N0  N1  N2  N3
  2P LOSS MUTATED    13   7   4   0
  2P LOSS WILD-TYPE 304 126  36   5
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              13               304
  N1               7               126
  N2               4                36
  N3               0                 5
[1] 4 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    21   0
  2P LOSS WILD-TYPE 390   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     21    0
  2P LOSS WILD-TYPE  390    7
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              21               390
  1               0                 7
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    10  14
  2P LOSS WILD-TYPE 120 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10   14
  2P LOSS WILD-TYPE  120  357
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              10               120
  MALE                14               357
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    17   1
  2P LOSS WILD-TYPE 367  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     17    1
  2P LOSS WILD-TYPE  367   52
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               17               367
  YES               1                52
[1] 2 2
[1] FALSE
D44V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED                                       1
  2P LOSS WILD-TYPE                                    14
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  2P LOSS MUTATED                                        0
  2P LOSS WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED                                         0
  2P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                            23
  2P LOSS WILD-TYPE                                                         456
D44V10, multiclass
                                                             clus
vv                                                            2P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              23
                                                             clus
vv                                                            2P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               456
[1] 4 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    21   0   0   1
  2P LOSS WILD-TYPE 378  12   4  22
D44V13, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              21               378
  R1               0                12
  R2               0                 4
  RX               1                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         2    18
  2P LOSS WILD-TYPE     9                        29   331
D44V14, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               2                29
  WHITE                                  18               331
[1] 3 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  16
  2P LOSS WILD-TYPE   7 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   16
  2P LOSS WILD-TYPE    7  301
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              16               301
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    28  16
  2Q LOSS WILD-TYPE 252 198
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               44               450 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               198 
$`2Q LOSS MUTATED`
TCGA-33-4533 TCGA-43-2578 TCGA-43-7657 TCGA-63-A5MH TCGA-94-A5I4 TCGA-NC-A5HM 
      133.74        22.49         7.76        66.61        16.14        39.85 
TCGA-NC-A5HR TCGA-18-3417 TCGA-18-3421 TCGA-21-1082 TCGA-21-5786 TCGA-21-5787 
       40.90        36.07        86.96       119.80        33.93        10.82 
TCGA-22-4594 TCGA-22-4604 TCGA-22-5481 TCGA-37-4141 TCGA-37-A5EN TCGA-39-5028 
       48.33        13.12        79.20         0.39        21.70         1.71 
TCGA-43-8115 TCGA-51-4081 TCGA-56-1622 TCGA-56-7823 TCGA-56-8304 TCGA-56-8307 
       13.38        29.95        28.96        33.24         3.48        26.89 
TCGA-56-A62T TCGA-58-8392 TCGA-58-A46K TCGA-60-2713 TCGA-60-2724 TCGA-63-A5MP 
       14.47        16.47        34.36        56.91        23.57        25.28 
TCGA-66-2763 TCGA-66-2767 TCGA-66-2800 TCGA-68-A59J TCGA-77-7465 TCGA-77-8007 
        0.99         2.01        49.05        14.73        32.55         6.51 
TCGA-77-8136 TCGA-85-7696 TCGA-85-7699 TCGA-85-8288 TCGA-85-8352 TCGA-85-8664 
       39.09        36.53        32.91        13.22         5.29        18.08 
TCGA-92-8064 TCGA-NK-A5CR 
        5.26        83.57 

$`2Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 
       27.19        32.19        14.93        48.82        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
       22.06       129.01         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
       31.27        17.88        18.38        78.18         2.93        11.61 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       12.03        19.99        13.05         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
       17.85        21.04         0.13         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32         8.02        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7545 
        9.50        14.07        21.04         0.16        18.38        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       19.36         2.76         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       76.80        65.65        16.80         0.43         8.58        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 
      117.57        11.34        23.54        92.15        92.42         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      154.32        49.94       119.54        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       60.89        34.78        15.58        31.73       122.43         9.34 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 
       43.23        31.63        88.11        41.69        21.99         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
        4.31        64.21         1.74        14.10        27.02        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 
       35.08        24.13         0.56        38.17        34.75        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       19.30         9.57        11.77        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        0.79        86.30        71.34        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        56.32        16.64        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        0.30        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       39.32         4.96         1.12        38.79         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       33.90         4.01         0.43         0.39         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 
        7.46         7.82         6.81         3.39        37.58       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        60.53        36.39        68.38        71.18 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       55.56        17.06        40.21        38.66        39.12        33.11 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       27.91        22.98        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       19.59        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       13.02         9.83         4.44        10.65        13.91         0.39 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
        0.39        28.34         5.46        30.35         8.75        27.45 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       12.43        18.25        21.90        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 
       30.41        19.76         6.51         0.10        17.49        14.96 
TCGA-56-8083 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
        4.93        14.07         1.35         1.81        22.75        13.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
       10.36         9.93        20.25        15.81        20.94        19.23 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       13.32        18.74         0.26         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
       29.95        71.24        34.78        85.12        56.65        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       29.92        21.11        12.23        10.22        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 
       92.71        21.93        80.45        49.48        66.54        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       48.49        42.64         3.19        29.85        35.90        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       11.34        89.29        78.28        16.37        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       34.59        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        1.02         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
       25.05         2.01         1.02         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       19.00         3.02         2.01        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
       12.00        24.95         1.97        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        4.04        22.98         5.03        30.02        10.06        54.08 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
        4.01         2.73         6.64         6.94        13.35        16.18 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       11.18       140.09         0.49        73.22        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        0.16        46.78        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       12.59        53.92        17.72       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       27.39         6.97        66.51        54.41        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       36.36       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       61.94        27.62        38.86         9.67        41.39        40.24 
TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
        6.41        34.95        31.30         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       18.94        25.15        19.04        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 
       30.64        34.52        10.09         0.76        22.45        16.77 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        3.09        32.71         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       38.14        12.59        22.59        30.28        34.13        30.97 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       19.86        24.36        30.48        19.73        27.16        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       15.85        14.96        15.29        29.92        12.39         3.65 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       24.92         2.93        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
        2.70         3.48         4.01         2.30         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
       26.63        14.14        17.69        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       27.68        21.44        30.81        30.67        21.34        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
       18.15         2.01        27.02        20.32        18.58        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       12.89        16.11        13.18        13.41        11.84         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       64.54         1.22        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX 
       49.28        43.92        25.32        14.73        26.43         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         3.72        12.72        43.89        11.18         0.20 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.39              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           133.74            173.82 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           26.085            21.275 
[1] "0.4 - 133.7 (26.1)" "0.0 - 173.8 (21.3)"
[1] "hr=" "1.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         0        6       11        0         8         7
  2Q LOSS WILD-TYPE       2       83      141        2        57        88
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  2Q LOSS MUTATED           0          7          3        1
  2Q LOSS WILD-TYPE         3         56         16        6
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 6                83
  STAGE IB                11               141
  STAGE II                 0                 2
  STAGE IIA                8                57
  STAGE IIB                7                88
  STAGE III                0                 3
  STAGE IIIA               7                56
  STAGE IIIB               3                16
  STAGE IV                 1                 6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     8  28   4   4
  2Q LOSS WILD-TYPE 104 266  67  20
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               8               104
  T2              28               266
  T3               4                67
  T4               4                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                 N0  N1  N2  N3
  2Q LOSS MUTATED    22  17   4   1
  2Q LOSS WILD-TYPE 295 116  36   4
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              22               295
  N1              17               116
  N2               4                36
  N3               1                 4
[1] 4 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    35   1
  2Q LOSS WILD-TYPE 376   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     35    1
  2Q LOSS WILD-TYPE  376    6
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              35               376
  1               1                 6
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    14  30
  2Q LOSS WILD-TYPE 116 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     14   30
  2Q LOSS WILD-TYPE  116  341
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              14               116
  MALE                30               341
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    33   4
  2Q LOSS WILD-TYPE 351  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     33    4
  2Q LOSS WILD-TYPE  351   49
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               33               351
  YES               4                49
[1] 2 2
[1] FALSE
D45V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED                                       2
  2Q LOSS WILD-TYPE                                    13
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  2Q LOSS MUTATED                                        0
  2Q LOSS WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED                                         0
  2Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                            42
  2Q LOSS WILD-TYPE                                                         437
D45V10, multiclass
                                                             clus
vv                                                            2Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              42
                                                             clus
vv                                                            2Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               437
[1] 4 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    37   1   0   2
  2Q LOSS WILD-TYPE 362  11   4  21
D45V13, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              37               362
  R1               1                11
  R2               0                 4
  RX               2                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         3    31
  2Q LOSS WILD-TYPE     9                        28   318
D45V14, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               3                28
  WHITE                                  31               318
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  29
  2Q LOSS WILD-TYPE   8 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   29
  2Q LOSS WILD-TYPE    8  288
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              29               288
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   176 130
  3P LOSS WILD-TYPE 104  84
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              306               188 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              130                84 
$`3P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI 
       12.20         4.47       123.19        31.99         6.18        32.19 
TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-34-2604 
       60.66        64.93        22.06       129.01         1.55        31.50 
TCGA-34-2605 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 
       28.96         7.76        78.18         2.93        11.61        19.99 
TCGA-56-8201 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 
       13.05        16.77        17.85        21.04         3.58        41.42 
TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-90-7766 TCGA-90-7964 
        9.01        32.32        66.61         8.02         9.50        14.07 
TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HE 
        0.16        16.14        19.36         5.69         0.07        76.80 
TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       39.85        65.65        16.80         8.58        75.75       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-4086 TCGA-18-4721 
       11.34        23.54        92.15        36.07         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 
       49.94       119.54        46.88        70.16        34.78        31.73 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 
      119.80        43.23        31.63        88.11        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
       21.99         7.33        14.10        27.02        20.48        48.33 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       38.17        13.12        32.02        19.30         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       63.55        14.63         0.79        86.30        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5492 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 
       11.74        18.84        16.64       151.27        54.44        63.35 
TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
        4.70        36.62        44.19        27.16         2.63        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5927 TCGA-34-5929 TCGA-34-8455 
       32.88        65.23        60.30        44.75         4.96         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4141 
       26.43        33.90         7.96         8.12         7.46         0.39 
TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 
        3.39        21.70       133.25       126.58        82.52       102.18 
TCGA-39-5028 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 TCGA-43-2581 
        1.71        60.53        68.38        71.18        40.21        38.66 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       33.11        22.98        21.47        19.59        13.38        11.77 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 
        0.39         0.39        29.95        28.34         5.46         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 
       27.45        28.96        12.43        21.90        18.48        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8304 
       30.41        19.76         0.10        17.49        33.24         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 
       26.89        14.07         1.35        13.81         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       15.81        19.23        13.32         0.26        14.47         0.03 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46K TCGA-60-2695 TCGA-60-2698 
       13.55        29.95        71.24        34.36        21.11        10.22 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 
       21.93        80.45        66.54        42.64        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 
       23.57        26.83        11.77        70.13        70.42        55.30 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MS 
       58.65        59.97        45.57        14.99        89.29        78.28 
TCGA-63-A5MT TCGA-66-2734 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
       16.37        43.10        21.07         2.01         0.92        43.99 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       21.01         0.99         2.01         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
       23.01         3.02        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 
       24.95        25.97        40.01        22.98        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       30.02        10.06         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 
        6.94        13.35        16.18        12.33        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       75.09        23.28        11.18       140.09         0.49        73.22 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8128 
       70.13       106.95         0.16        46.78        32.55        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
      156.66        53.92        17.72       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 
       27.39        66.51        65.49        60.53        36.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 
       22.29         5.92        38.86         9.67        41.39        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 
       31.30        32.91         1.38        29.95        18.94        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 TCGA-85-8351 
       31.56        26.79        30.64        10.09        13.22        16.77 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8666 TCGA-85-A4CL 
        3.09         2.01        15.39         7.76        22.59        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
       34.13        30.97        30.48        19.73        16.21        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED 
       14.96        15.29        12.39         3.65         2.93        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       22.62        10.59         3.48         4.01         5.26         2.30 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        5.03        26.63        14.14        17.69        71.01        18.31 
TCGA-96-8170 TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J 
       17.46        30.81        21.34        18.15        18.58        20.71 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       12.89        13.18        11.84         4.54        64.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       13.74         2.89        49.28        43.92        25.32        14.73 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       83.57         3.65         3.72        12.72        43.89        11.18 

$`3P LOSS WILD-TYPE`
TCGA-18-3410 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-33-4533 TCGA-33-6737 
        4.80        27.19        14.93        48.82       133.74        19.76 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-A56V TCGA-56-8305 
       31.27        17.88        22.49        18.38        12.03         3.45 
TCGA-56-8308 TCGA-56-A5DR TCGA-60-2715 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       17.00         0.13        35.34        20.78        42.08        30.81 
TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH 
       21.04        18.38        57.07         2.76        21.21        19.10 
TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3419 TCGA-18-3421 TCGA-21-1072 TCGA-21-1076 
       40.90         0.43        92.42        86.96        99.16        60.89 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5784 TCGA-22-1002 TCGA-22-1005 
       15.58       122.43         9.34        41.69         4.31        64.21 
TCGA-22-1011 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-5477 
        1.74        35.08        24.13         0.56        34.75        44.25 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       30.12        62.86        56.32        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4586 TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ 
      103.53        14.07         0.30         6.94       110.99       118.36 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 
       81.24        74.66         9.07        50.66        16.93        39.32 
TCGA-34-7107 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4133 
        1.12        38.79         4.01         0.43         0.39         7.82 
TCGA-37-4135 TCGA-37-A5EL TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5029 
        6.81        37.58       111.35        68.58        55.20        24.33 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 TCGA-43-3394 TCGA-43-5670 
        1.94        36.39        55.56        17.06        39.12        27.91 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
       24.89         5.46         3.81         9.73        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       12.16        13.02         9.83         4.44        10.65        13.91 
TCGA-52-7810 TCGA-56-5898 TCGA-56-7223 TCGA-56-7730 TCGA-56-8082 TCGA-56-8083 
       30.35        18.25        14.53         6.51        14.96         4.93 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4ZK TCGA-58-8387 
        1.81        22.75        10.36        20.94        18.74        13.25 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       16.47        34.78        85.12        56.65        35.24        29.92 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2709 TCGA-60-2713 
       12.23        96.82        37.94        92.71        49.48        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-63-6202 TCGA-63-7022 TCGA-63-A5MB 
       50.33        48.49         3.19        52.67        68.15       102.67 
TCGA-63-A5MG TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       70.62        11.34        25.28        36.16        53.88        34.59 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2756 TCGA-66-2759 
       16.96         2.01         0.99         1.02         0.99        25.05 
TCGA-66-2766 TCGA-66-2771 TCGA-66-2777 TCGA-66-2785 TCGA-66-2789 TCGA-66-2794 
        1.02        19.00         2.01         1.97         4.04        54.08 
TCGA-68-A59J TCGA-70-6722 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8131 
       14.73        12.07         6.51        86.76        55.73        12.59 
TCGA-77-8136 TCGA-77-8145 TCGA-77-8150 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 
       39.09         6.97        54.41       126.18       132.36        61.94 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7843 TCGA-85-8048 
       27.62        40.24         6.41        36.53         1.15        25.15 
TCGA-85-8049 TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 
       19.04        34.52         0.76        22.45         5.29        32.71 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4JC TCGA-85-A4PA 
       36.59        38.14        12.59        18.08        19.86        24.36 
TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 TCGA-94-8035 
       27.16        29.92        24.92        11.77         2.70         4.01 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53C 
       27.68        21.44        30.67        27.16         2.01        27.02 
TCGA-98-A53H TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HT 
       20.32        16.11        13.41         1.22         4.21        26.43 
TCGA-O2-A52N TCGA-XC-AA0X 
       33.07         0.20 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.03              0.13 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           156.66            173.82 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           21.585            22.470 
[1] "0.0 - 156.7 (21.6)" "0.1 - 173.8 (22.5)"
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         1       55       96        1        41        54
  3P LOSS WILD-TYPE       1       34       56        1        24        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  3P LOSS MUTATED           3         36         13        7
  3P LOSS WILD-TYPE         0         27          6        0
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                55                34
  STAGE IB                96                56
  STAGE II                 1                 1
  STAGE IIA               41                24
  STAGE IIB               54                41
  STAGE III                3                 0
  STAGE IIIA              36                27
  STAGE IIIB              13                 6
  STAGE IV                 7                 0
[1] 10  2
[1] 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    70 181  43  16
  3P LOSS WILD-TYPE  42 113  28   8
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              70                42
  T2             181               113
  T3              43                28
  T4              16                 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
  3P LOSS MUTATED   198  84  23   4
  3P LOSS WILD-TYPE 119  49  17   1
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0             198               119
  N1              84                49
  N2              23                17
  N3               4                 1
[1] 4 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   252   7
  3P LOSS WILD-TYPE 159   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    252    7
  3P LOSS WILD-TYPE  159    0
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             252               159
  1               7                 0
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    85 225
  3P LOSS WILD-TYPE  45 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     85  225
  3P LOSS WILD-TYPE   45  146
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              85                45
  MALE               225               146
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   246  31
  3P LOSS WILD-TYPE 138  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    246   31
  3P LOSS WILD-TYPE  138   22
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO              246               138
  YES              31                22
[1] 2 2
[1] FALSE
D46V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                      10
  3P LOSS WILD-TYPE                                     5
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  3P LOSS MUTATED                                        3
  3P LOSS WILD-TYPE                                      3
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                         1
  3P LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                           296
  3P LOSS WILD-TYPE                                                         183
D46V10, multiclass
                                                             clus
vv                                                            3P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             296
                                                             clus
vv                                                            3P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               183
[1] 4 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   245   4   3  14
  3P LOSS WILD-TYPE 154   8   1   9
D46V13, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0             245               154
  R1               4                 8
  R2               3                 1
  RX              14                 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                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       4                        17   216
  3P LOSS WILD-TYPE     5                        14   133
D46V14, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              17                14
  WHITE                                 216               133
[1] 3 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     6 186
  3P LOSS WILD-TYPE   2 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6  186
  3P LOSS WILD-TYPE    2  131
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO             186               131
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    38  33
  3Q LOSS WILD-TYPE 242 181
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               71               423 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               33               181 
$`3Q LOSS MUTATED`
TCGA-18-3416 TCGA-43-A474 TCGA-56-7221 TCGA-60-2696 TCGA-94-7557 TCGA-94-A5I4 
       31.99        11.61        19.99         3.58         0.16        16.14 
TCGA-98-A539 TCGA-NC-A5HE TCGA-18-3408 TCGA-18-3412 TCGA-18-5592 TCGA-21-1075 
        5.69        76.80        75.75        11.34        49.94        70.16 
TCGA-21-1079 TCGA-21-1082 TCGA-22-0944 TCGA-22-1016 TCGA-22-4594 TCGA-22-4604 
       31.73       119.80         7.33        27.02        48.33        13.12 
TCGA-22-5483 TCGA-22-5492 TCGA-33-4583 TCGA-33-6738 TCGA-34-5929 TCGA-37-4129 
       18.84        16.64       151.27        63.35         4.96         7.96 
TCGA-37-A5EN TCGA-39-5011 TCGA-39-5027 TCGA-43-2581 TCGA-51-4079 TCGA-52-7811 
       21.70       133.25       102.18        38.66         0.39         8.75 
TCGA-56-1622 TCGA-56-7579 TCGA-56-7582 TCGA-56-8307 TCGA-56-8503 TCGA-58-8388 
       28.96        31.27        19.76        26.89         1.35        13.55 
TCGA-60-2698 TCGA-60-2722 TCGA-63-7021 TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM 
       10.22        29.85        70.42        58.65        59.97        14.99 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2769 TCGA-66-2782 TCGA-66-2788 TCGA-66-2791 
        2.01        43.99         7.07        12.00        22.98         5.03 
TCGA-66-2793 TCGA-66-2795 TCGA-70-6723 TCGA-77-6843 TCGA-77-6844 TCGA-77-8130 
       10.06         4.01        12.33        73.12        75.09       156.66 
TCGA-77-8154 TCGA-85-6175 TCGA-85-7698 TCGA-85-8070 TCGA-85-8071 TCGA-85-8355 
       60.53         9.67        31.30        31.56        26.79         2.01 
TCGA-85-8481 TCGA-85-A4CN TCGA-85-A50Z TCGA-85-A53L TCGA-90-A4ED TCGA-92-7341 
        7.76        34.13        16.21        12.39        20.22         3.48 
TCGA-96-8169 TCGA-98-8023 TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-O2-A5IB 
       18.31        21.34         2.89        14.73        11.18 

$`3Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19         4.80         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
      129.01       133.74         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       31.27        17.88        22.49        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
        2.93        12.03        13.05         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.85        21.04         0.13        41.42         9.01        35.34 
TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       32.32        66.61         8.02        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JK 
        9.50        14.07        21.04        18.38        57.07        19.36 
TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR 
        2.76        21.21        19.10         0.07        39.85        40.90 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3414 
       65.65        16.80         0.43         8.58       117.57        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       92.15        36.07        92.42        86.96         2.79       154.32 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
      119.54        46.88        99.16        60.89        34.78        15.58 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
      122.43         9.34        43.23        31.63        88.11        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       33.93        10.82        21.99         4.31        64.21         1.74 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       14.10        20.48        35.08        24.13         0.56        38.17 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       34.75        32.02        19.30         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       14.63        44.25         0.79        86.30        71.34        79.20 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 
       11.74        30.12        62.86        56.32        97.94        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW 
      173.82       103.53        14.07        54.44         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
       36.62         6.94       110.99        44.19       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        2.63        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        60.30        50.66        16.93        44.75        39.32 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        38.79         4.04        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         0.39         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        0.39         3.39        37.58       126.58       111.35        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       55.20        82.52         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       36.39        68.38        71.18        55.56        17.06        40.21 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       39.12        33.11        27.91        22.98        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
        5.46         3.81        19.59        13.38        11.77         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       14.20        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65        13.91         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
       30.35        27.45        12.43        18.25        21.90        18.48 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       14.53        30.41         6.51         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 
       14.96         4.93         3.48        14.07         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
       13.81        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       19.23        13.32        18.74         0.26        14.47         0.03 
TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       13.25        29.95        71.24        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       34.36        56.65        35.24        29.92        21.11        12.23 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       96.82        37.94        92.71        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       66.54        56.91        50.33        48.49        42.64         3.19 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
       35.90        23.57        26.83        11.77        52.67        70.13 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5ML TCGA-63-A5MN 
       68.15        55.30       102.67        70.62        45.57        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       25.28        89.29        78.28        16.37        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       34.59        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        1.02         0.92         0.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 
        2.01         1.02         2.01         2.01        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 
        3.02         2.01        19.00        12.03         3.98        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 
        1.97        25.97        40.01         4.04        22.98        30.02 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
       54.08        49.05         2.73         6.64         6.94        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 
       16.18        14.73        12.07        29.56        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
       46.78        32.55         6.51        86.76        55.73        37.81 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       12.59        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       26.40        27.39         6.97        66.51        54.41        65.49 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       36.36       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
       61.94        27.62        38.86        41.39        40.24         6.41 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       36.53        34.95        32.91         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 
       18.94        25.15        19.04        24.13        30.64        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       10.09         0.76        13.22        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        3.09        32.71        15.39        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
       18.08        22.59        30.28        30.97        19.86        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
       30.48        19.73        27.16        15.85        14.96        15.29 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
       29.92         3.65        24.92         2.93        11.77        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
       10.59         2.70         4.01         5.26         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 
        5.03        26.63        14.14        17.69        71.01        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A 
       27.68        21.44        30.81        30.67        27.16        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
        2.01        27.02        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG 
       16.11        13.18        13.41        11.84         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO 
        1.22        57.30        13.74         4.21        49.28        43.92 
TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q 
       25.32        26.43        83.57         3.65        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       12.72        43.89         0.20 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.16              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           156.66            173.82 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            19.76             22.29 
[1] "0.2 - 156.7 (19.8)" "0.0 - 173.8 (22.3)"
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         0        9       18        0        11        17
  3Q LOSS WILD-TYPE       2       80      134        2        54        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  3Q LOSS MUTATED           1         12          5        0
  3Q LOSS WILD-TYPE         2         51         14        7
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 9                80
  STAGE IB                18               134
  STAGE II                 0                 2
  STAGE IIA               11                54
  STAGE IIB               17                78
  STAGE III                1                 2
  STAGE IIIA              12                51
  STAGE IIIB               5                14
  STAGE IV                 0                 7
[1] 10  2
[1] 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    13  39  17   4
  3Q LOSS WILD-TYPE  99 255  54  20
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              13                99
  T2              39               255
  T3              17                54
  T4               4                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                 N0  N1  N2  N3
  3Q LOSS MUTATED    42  23   7   1
  3Q LOSS WILD-TYPE 275 110  33   4
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              42               275
  N1              23               110
  N2               7                33
  N3               1                 4
[1] 4 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    67   0
  3Q LOSS WILD-TYPE 344   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     67    0
  3Q LOSS WILD-TYPE  344    7
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              67               344
  1               0                 7
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    17  56
  3Q LOSS WILD-TYPE 113 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     17   56
  3Q LOSS WILD-TYPE  113  315
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              17               113
  MALE                56               315
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    56   8
  3Q LOSS WILD-TYPE 328  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     56    8
  3Q LOSS WILD-TYPE  328   45
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               56               328
  YES               8                45
[1] 2 2
[1] FALSE
D47V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED                                       1
  3Q LOSS WILD-TYPE                                    14
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  3Q LOSS MUTATED                                        2
  3Q LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED                                         0
  3Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                            70
  3Q LOSS WILD-TYPE                                                         409
D47V10, multiclass
                                                             clus
vv                                                            3Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              70
                                                             clus
vv                                                            3Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               409
[1] 4 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    60   2   0   4
  3Q LOSS WILD-TYPE 339  10   4  19
D47V13, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              60               339
  R1               2                10
  R2               0                 4
  RX               4                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       2                         3    48
  3Q LOSS WILD-TYPE     7                        28   301
D47V14, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               3                28
  WHITE                                  48               301
[1] 3 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     1  42
  3Q LOSS WILD-TYPE   7 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   42
  3Q LOSS WILD-TYPE    7  275
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              42               275
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   175 135
  4P LOSS WILD-TYPE 105  79
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              310               184 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              135                79 
$`4P LOSS MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-4083 TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 
        4.47        31.99         6.18        14.93        60.66        64.93 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-43-2578 
      129.01       133.74         1.55        19.76        28.96        22.49 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 
        7.76         2.93        11.61        12.03        19.99        13.05 
TCGA-56-8308 TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 
       17.00         0.13         3.58        41.42         9.01        32.32 
TCGA-63-A5MH TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7557 
       66.61        42.08        30.81         9.50        14.07         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD 
       18.38        16.14        19.36         2.76         5.69         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-O2-A52W TCGA-18-3411 
       76.80        39.85        40.90        65.65         8.58       117.57 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 
       11.34        92.15        36.07        86.96         2.79        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 
      119.54        46.88        99.16        60.89        34.78        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 
      122.43         9.34       119.80        43.23        31.63        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 
       10.82        21.99         7.33         1.74        14.10        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       48.33        24.13        38.17        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 
        9.57        63.55        14.63        44.25        86.30        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 
       18.84        30.12        62.86        56.32        97.94        79.53 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         4.70 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
       36.62         6.94       110.99        44.19       118.36        27.16 
TCGA-34-2600 TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 
       61.61        65.23        81.24         9.07        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 
       39.32         4.96         1.12        26.43         4.01         0.43 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN 
        7.82         6.81         0.39         3.39        37.58        21.70 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 TCGA-39-5034 
      126.58       111.35        68.58       102.18        60.53        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-3394 TCGA-43-6143 TCGA-43-6771 
       68.38        55.56        17.06        39.12        22.98         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-A56U TCGA-46-3765 TCGA-46-3768 
        3.81        19.59        13.38        14.20        13.32         9.83 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
       10.65        13.91        29.95         5.46        30.35         8.75 
TCGA-52-7812 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       27.45        18.25        21.90        18.48        14.53        31.27 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 TCGA-56-8625 
       19.76         6.51        33.24         4.93         3.48        10.36 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8387 
       20.94        19.23        13.32        18.74        14.47        13.25 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       16.47        34.78        85.12        34.36        56.65        35.24 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       21.11        10.22        96.82        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
       49.48        66.54        56.91        50.33        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 
       29.85        35.90        23.57        11.77        70.13        70.42 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS 
       55.30       102.67        59.97        45.57        89.29        78.28 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
       34.59        16.96        43.10         2.01        21.07         1.02 
TCGA-66-2754 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2767 TCGA-66-2771 
        2.01        21.01        25.05         2.01         2.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 
        3.02         2.01        19.00        12.03         3.98        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        1.97        25.97         5.03        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59J TCGA-70-6723 
        4.01        49.05         2.73         6.64        14.73        12.33 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       73.12        23.28       140.09         0.49        73.22        70.13 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 
       46.78        32.55        55.73        37.81       156.66        53.92 
TCGA-77-8138 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       17.72        27.39         6.97        66.51        54.41        65.49 
TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH 
       60.53       150.25         5.92        61.94        27.62        38.86 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       41.39        40.24        36.53        34.95        31.30        32.91 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
        1.15        25.15        19.04        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       30.64        34.52        10.09         0.76        13.22        22.45 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
        5.29         3.09        32.71        36.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A512 
       30.28        34.13        30.48        19.73        15.85        15.29 
TCGA-85-A53L TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       12.39        20.22        22.62        10.59         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-A5I6 
        4.01         5.26         2.30         4.01         5.03        17.69 
TCGA-98-7454 TCGA-98-8021 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I 
       21.44        30.81        27.16        18.15         2.01        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54        64.54        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX 
       49.28        43.92        25.32        14.73        83.57         3.65 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89        11.18         0.20 

$`4P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1017 
       12.20       123.19         4.80        27.19        32.19        48.82 
TCGA-22-A5C4 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7658 
       22.06        31.50        31.27        17.88        18.38        78.18 
TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2715 TCGA-68-8250 
        3.45        16.77        17.85        21.04        35.34         8.02 
TCGA-77-7140 TCGA-94-7033 TCGA-96-7545 TCGA-98-A53D TCGA-J1-A4AH TCGA-NK-A5D1 
       20.78        21.04        57.07        21.21        19.10        16.80 
TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3414 TCGA-18-3419 TCGA-18-4721 TCGA-21-1075 
        0.43        75.75        23.54        92.42       154.32        70.16 
TCGA-21-1078 TCGA-21-5783 TCGA-21-5784 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 
       15.58        88.11        41.69         4.31        64.21        27.02 
TCGA-22-4591 TCGA-22-4596 TCGA-22-4601 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 
       20.48         0.56        34.75        11.77         0.79        71.34 
TCGA-22-5481 TCGA-22-5492 TCGA-33-4566 TCGA-33-A5GW TCGA-34-2596 TCGA-34-2608 
       79.20        16.64       173.82         0.30         2.63        32.88 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX 
       74.66        60.30        50.66        38.79         4.04        33.90 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5022 
        0.39         7.96         8.12         7.46       133.25        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5036 TCGA-43-2576 
       82.52         1.71        24.33         1.94        71.18        40.21 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-8116 
       38.66        33.11        27.91        24.89        21.47        11.77 
TCGA-43-A475 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-51-4079 TCGA-51-4080 
        9.73        12.16        13.02         4.44         0.39         0.39 
TCGA-52-7622 TCGA-56-1622 TCGA-56-5897 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 
       28.34        28.96        12.43        30.41         0.10        17.49 
TCGA-56-8082 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
       14.96        26.89        14.07         1.35         1.81        22.75 
TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A5DS TCGA-58-8386 
       13.81         9.93        20.25        15.81         0.26         0.03 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46N TCGA-60-2697 TCGA-60-2704 
       13.55        29.95        71.24        29.92        12.23        37.94 
TCGA-60-2716 TCGA-60-2725 TCGA-63-6202 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI 
       48.49        26.83        52.67        68.15        70.62        58.65 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       14.99        11.34        25.28        16.37        36.16        53.88 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2766 
        0.99         0.92         0.99        43.99         0.99         1.02 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 TCGA-66-2787 TCGA-66-2788 
        2.01         7.07        23.01        12.00        40.01        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-70-6722 
        4.04        22.98         6.94        13.35        16.18        12.07 
TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 
       29.56        75.09        11.18       106.95         0.16         6.51 
TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       86.76        12.59        39.09       104.09        11.54        26.40 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-85-6175 TCGA-85-6798 
       36.36       126.18       132.36        22.29         9.67         6.41 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8351 TCGA-85-8355 TCGA-85-8479 
        1.38        29.95        18.94        16.77         2.01        15.39 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
        7.76        38.14        12.59        30.97        19.86        24.36 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 
       27.16        16.21        14.96        29.92         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        2.93        11.77        26.63        14.14        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-8022 TCGA-98-8023 TCGA-98-A53C TCGA-98-A53H 
       17.46        27.68        30.67        21.34        27.02        20.32 
TCGA-NC-A5HH TCGA-NC-A5HT TCGA-O2-A52N TCGA-O2-A52Q 
        1.22        26.43        33.07         3.72 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.07              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           156.66            173.82 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            22.54             20.91 
[1] "0.1 - 156.7 (22.5)" "0.0 - 173.8 (20.9)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         1       47      107        2        43        54
  4P LOSS WILD-TYPE       1       42       45        0        22        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  4P LOSS MUTATED           2         40         13        3
  4P LOSS WILD-TYPE         1         23          6        4
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                47                42
  STAGE IB               107                45
  STAGE II                 2                 0
  STAGE IIA               43                22
  STAGE IIB               54                41
  STAGE III                2                 1
  STAGE IIIA              40                23
  STAGE IIIB              13                 6
  STAGE IV                 3                 4
[1] 10  2
[1] 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    64 194  44  13
  4P LOSS WILD-TYPE  48 100  27  11
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              64                48
  T2             194               100
  T3              44                27
  T4              13                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
  4P LOSS MUTATED   195  86  27   4
  4P LOSS WILD-TYPE 122  47  13   1
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0             195               122
  N1              86                47
  N2              27                13
  N3               4                 1
[1] 4 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   258   3
  4P LOSS WILD-TYPE 153   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    258    3
  4P LOSS WILD-TYPE  153    4
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             258               153
  1               3                 4
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    78 237
  4P LOSS WILD-TYPE  52 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     78  237
  4P LOSS WILD-TYPE   52  134
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              78                52
  MALE               237               134
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   239  40
  4P LOSS WILD-TYPE 145  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    239   40
  4P LOSS WILD-TYPE  145   13
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              239               145
  YES              40                13
[1] 2 2
[1] FALSE
D48V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                       8
  4P LOSS WILD-TYPE                                     7
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  4P LOSS MUTATED                                        1
  4P LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                         1
  4P LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                           305
  4P LOSS WILD-TYPE                                                         174
D48V10, multiclass
                                                             clus
vv                                                            4P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             305
                                                             clus
vv                                                            4P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               174
[1] 4 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   250   7   4  16
  4P LOSS WILD-TYPE 149   5   0   7
D48V13, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0             250               149
  R1               7                 5
  R2               4                 0
  RX              16                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       3                        23   221
  4P LOSS WILD-TYPE     6                         8   128
D48V14, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              23                 8
  WHITE                                 221               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     5 195
  4P LOSS WILD-TYPE   3 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5  195
  4P LOSS WILD-TYPE    3  122
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             195               122
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   164 129
  4Q LOSS WILD-TYPE 116  85
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              293               201 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              129                85 
$`4Q LOSS MUTATED`
TCGA-18-3407 TCGA-18-4083 TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 
        4.47         6.18        14.93        60.66        64.93       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-43-2578 TCGA-43-7657 
      133.74         1.55        19.76        28.96        22.49         7.76 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 
       78.18         2.93        11.61        12.03        19.99        13.05 
TCGA-56-8308 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 TCGA-60-2721 
       17.00        21.04         0.13         3.58         9.01        32.32 
TCGA-63-A5MH TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7557 TCGA-94-7943 
       66.61        42.08        30.81        14.07         0.16        18.38 
TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
       16.14        19.36         5.69         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
       40.90        65.65         8.58       117.57        11.34        92.15 
TCGA-18-3417 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       36.07         2.79       154.32        49.94       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 
       99.16        70.16        60.89        34.78        31.73       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 
        9.34       119.80        43.23        31.63        33.93        10.82 
TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
        7.33         1.74        14.10        48.33        24.13        38.17 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       13.12        32.02        19.30        11.77        63.55        14.63 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       86.30        11.74        18.84        30.12        62.86        56.32 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       97.94       173.82       103.53       151.27        14.07        54.44 
TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
        4.70        36.62         6.94        44.19       118.36        27.16 
TCGA-34-2600 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       61.61         9.07        16.93        44.75        39.32         4.96 
TCGA-34-7107 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        1.12         7.82         6.81         0.39         3.39        37.58 
TCGA-37-A5EN TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 TCGA-39-5034 
       21.70       111.35        68.58       102.18        60.53        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-3394 TCGA-43-6143 
       68.38        71.18        55.56        17.06        39.12        22.98 
TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-A56U TCGA-46-3765 TCGA-46-3768 
        5.46         3.81        13.38        14.20        13.32         9.83 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
       10.65        13.91         0.39        29.95         5.46        30.35 
TCGA-52-7811 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 
        8.75        18.25        21.90        18.48        14.53        19.76 
TCGA-56-7730 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 TCGA-56-8625 TCGA-56-8629 
        6.51        33.24         4.93         3.48        10.36        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8390 TCGA-58-8392 
       20.94        13.32        18.74        14.47        29.95        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
       34.78        85.12        34.36        56.65        35.24        21.11 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       10.22        96.82        92.71        21.93        80.45        49.48 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       56.91        50.33        42.64         3.19        29.85        35.90 
TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MB 
       23.57        11.77        70.13        70.42        55.30       102.67 
TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       70.62        59.97        45.57        89.29        78.28        16.37 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       53.88        34.59        16.96        43.10         2.01        21.07 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 
        1.02         2.01        43.99        21.01         0.99         2.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       19.00         3.02         2.01        19.00        12.03         3.98 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        1.97        25.97         5.03        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I 
        4.01        49.05         2.73         6.64         6.94        16.18 
TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 
       14.73        12.07        12.33        73.12        23.28       140.09 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 
        0.49        73.22        46.78        32.55         6.51        55.73 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8144 
       37.81       156.66        53.92        39.09        17.72        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 
        6.97        66.51        54.41        65.49        60.53       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
       22.29         5.92        61.94        27.62        38.86        41.39 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-8048 TCGA-85-8049 
       40.24         6.41        36.53        32.91        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       24.13        31.56        30.64        34.52        10.09         0.76 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 
       22.45         5.29         3.09        15.39        36.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
       22.59        30.28        34.13        30.48        19.73        15.85 
TCGA-85-A512 TCGA-85-A53L TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       15.29        12.39        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-A5I6 
        2.70         4.01         5.26         2.30         4.01        17.69 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I 
       21.44        30.81        30.67        27.16         2.01        18.58 
TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HI 
       20.71        16.11        13.18        11.84         4.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       13.74         4.21         2.89        43.92        25.32        14.73 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       83.57         3.65        12.72        43.89         0.20 

$`4Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19         4.80        31.99        27.19        32.19 
TCGA-22-1017 TCGA-22-A5C4 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 
       48.82        22.06        31.50        31.27        17.88        18.38 
TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2711 TCGA-60-2715 TCGA-68-8250 
        3.45        16.77        17.85        41.42        35.34         8.02 
TCGA-77-7140 TCGA-90-7766 TCGA-94-7033 TCGA-96-7545 TCGA-98-8020 TCGA-98-A53D 
       20.78         9.50        21.04        57.07         2.76        21.21 
TCGA-J1-A4AH TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3414 TCGA-18-3419 
       19.10        16.80         0.43        75.75        23.54        92.42 
TCGA-18-3421 TCGA-21-1078 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-1002 
       86.96        15.58        88.11        41.69        21.99         4.31 
TCGA-22-1005 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 
       64.21        27.02        20.48        35.08         0.56        34.75 
TCGA-22-4609 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 
        9.57        44.25         0.79        71.34        79.20        16.64 
TCGA-33-4547 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AASD TCGA-34-2596 TCGA-34-2608 
       79.53        63.35         0.30       110.99         2.63        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 
       65.23        81.24        74.66        60.30        50.66        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
        4.04        26.43        33.90         4.01         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 
        7.96         8.12         7.46       133.25       126.58        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-43-2576 TCGA-43-2581 
       82.52         1.71        24.33         1.94        40.21        38.66 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 
       33.11        27.91        24.89        21.47        19.59        11.77 
TCGA-43-A475 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-51-4080 TCGA-52-7622 
        9.73        12.16        13.02         4.44         0.39        28.34 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 
       27.45        28.96        12.43        31.27        30.41         0.10 
TCGA-56-7822 TCGA-56-8082 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
       17.49        14.96        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A5DS 
       22.75        13.81         9.93        20.25        19.23         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 TCGA-58-A46N TCGA-60-2697 
        0.03        13.25        13.55        71.24        29.92        12.23 
TCGA-60-2704 TCGA-60-2710 TCGA-60-2716 TCGA-60-2725 TCGA-63-6202 TCGA-63-7022 
       37.94        66.54        48.49        26.83        52.67        68.15 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MV TCGA-66-2744 
       58.65        14.99        11.34        25.28        36.16         0.99 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
        0.92         0.99        25.05         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 TCGA-66-2783 TCGA-66-2787 TCGA-66-2788 
        7.07        23.01        12.00        24.95        40.01        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-68-8251 TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 
        4.04        22.98        13.35        29.56        75.09        11.18 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8008 TCGA-77-8131 TCGA-77-8139 
       70.13       106.95         0.16        86.76        12.59       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-6175 
       11.54        26.40        36.36       126.18       132.36         9.67 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
       34.95        31.30         1.38         1.15        29.95        18.94 
TCGA-85-8071 TCGA-85-8288 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
       26.79        13.22        16.77        32.71         2.01         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M 
       38.14        12.59        30.97        19.86        24.36        27.16 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 
       16.21        14.96        29.92         3.65        24.92         2.93 
TCGA-92-7341 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        3.48         5.03        26.63        14.14        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-8023 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H 
       17.46        27.68        21.34        18.15        27.02        20.32 
TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HN TCGA-NC-A5HT 
       12.89        13.41        64.54         1.22        49.28        26.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A5IB 
       33.07         3.72        11.18 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.07              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           173.82            133.25 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            21.90             21.47 
[1] "0.1 - 173.8 (21.9)" "0.0 - 133.2 (21.5)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         1       48      105        2        33        56
  4Q LOSS WILD-TYPE       1       41       47        0        32        39
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  4Q LOSS MUTATED           1         36         10        3
  4Q LOSS WILD-TYPE         2         27          9        4
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                48                41
  STAGE IB               105                47
  STAGE II                 2                 0
  STAGE IIA               33                32
  STAGE IIB               56                39
  STAGE III                1                 2
  STAGE IIIA              36                27
  STAGE IIIB              10                 9
  STAGE IV                 3                 4
[1] 10  2
[1] 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    59 185  41  12
  4Q LOSS WILD-TYPE  53 109  30  12
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              59                53
  T2             185               109
  T3              41                30
  T4              12                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
  4Q LOSS MUTATED   193  78  21   2
  4Q LOSS WILD-TYPE 124  55  19   3
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0             193               124
  N1              78                55
  N2              21                19
  N3               2                 3
[1] 4 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   244   3
  4Q LOSS WILD-TYPE 167   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    244    3
  4Q LOSS WILD-TYPE  167    4
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             244               167
  1               3                 4
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    78 219
  4Q LOSS WILD-TYPE  52 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     78  219
  4Q LOSS WILD-TYPE   52  152
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              78                52
  MALE               219               152
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   224  37
  4Q LOSS WILD-TYPE 160  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    224   37
  4Q LOSS WILD-TYPE  160   16
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              224               160
  YES              37                16
[1] 2 2
[1] FALSE
D49V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                       6
  4Q LOSS WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  4Q LOSS MUTATED                                        2
  4Q LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                         1
  4Q LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                           288
  4Q LOSS WILD-TYPE                                                         191
D49V10, multiclass
                                                             clus
vv                                                            4Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
                                                             clus
vv                                                            4Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               191
[1] 4 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   235   7   3  17
  4Q LOSS WILD-TYPE 164   5   1   6
D49V13, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             235               164
  R1               7                 5
  R2               3                 1
  RX              17                 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                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       4                        20   202
  4Q LOSS WILD-TYPE     5                        11   147
D49V14, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              20                11
  WHITE                                 202               147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     4 180
  4Q LOSS WILD-TYPE   4 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4  180
  4Q LOSS WILD-TYPE    4  137
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO             180               137
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    49  29
  5P LOSS WILD-TYPE 231 185
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               78               416 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               29               185 
$`5P LOSS MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-22-5472 TCGA-33-4532 TCGA-33-6737 
      123.19         4.80         6.18        64.93       129.01        19.76 
TCGA-34-2605 TCGA-43-2578 TCGA-43-8118 TCGA-56-7221 TCGA-56-8308 TCGA-68-8250 
       28.96        22.49         2.93        19.99        17.00         8.02 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-94-A5I4 TCGA-NC-A5HM TCGA-NC-A5HR 
       14.07        21.04        18.38        16.14        39.85        40.90 
TCGA-18-3415 TCGA-21-1070 TCGA-21-1079 TCGA-22-4607 TCGA-22-5479 TCGA-22-5485 
       92.15       119.54        31.73        19.30        86.30        30.12 
TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-A5GW TCGA-34-5231 TCGA-37-4130 
       56.32        97.94        79.53         0.30        65.23         8.12 
TCGA-37-A5EN TCGA-39-5037 TCGA-46-3765 TCGA-51-4079 TCGA-52-7810 TCGA-56-5897 
       21.70        55.56        13.32         0.39        30.35        12.43 
TCGA-56-5898 TCGA-56-7730 TCGA-56-8082 TCGA-56-8622 TCGA-56-A49D TCGA-58-A46L 
       18.25         6.51        14.96         1.81        20.94        56.65 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2713 TCGA-60-2722 
       92.71        21.93        80.45        66.54        56.91        29.85 
TCGA-63-7023 TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2734 TCGA-66-2755 TCGA-66-2780 
       55.30        16.37        34.59        43.10         0.92        12.03 
TCGA-66-2785 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-68-8251 TCGA-70-6723 
        1.97         4.04         5.03        10.06        13.35        12.33 
TCGA-77-7139 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-85-6561 TCGA-85-7698 
      140.09        66.51        65.49        60.53        40.24        31.30 
TCGA-85-7950 TCGA-85-8276 TCGA-85-8288 TCGA-85-8352 TCGA-85-8355 TCGA-92-8063 
       18.94        34.52        13.22         5.29         2.01         4.01 
TCGA-98-A538 TCGA-LA-A7SW TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-O2-A52S 
       27.16        13.41        64.54        57.30         2.89        12.72 

$`5P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20         4.47        31.99        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 
       48.82        60.66        22.06       133.74         1.55        31.50 
TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 
       31.27        17.88        18.38         7.76        78.18        11.61 
TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ 
       12.03        13.05         3.45        16.77        17.85        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 
        0.13         3.58        41.42         9.01        35.34        32.32 
TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-94-7557 
       66.61        20.78        42.08        30.81         9.50         0.16 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH 
       57.07        19.36         2.76         5.69        21.21        19.10 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
        0.07        76.80        65.65        16.80         0.43         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 
       75.75       117.57        11.34        23.54        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 
       86.96         2.79       154.32        49.94        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
       70.16        60.89        34.78        15.58       122.43         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
      119.80        43.23        31.63        88.11        41.69        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       10.82        21.99         7.33         4.31        64.21         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
       14.10        27.02        20.48        35.08        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 
        0.56        38.17        34.75        13.12        32.02         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 
       11.77        63.55        14.63        44.25         0.79        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5492 TCGA-33-4566 
       79.20        11.74        18.84        62.86        16.64       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         4.70 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
       36.62         6.94       110.99        44.19       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
        2.63        61.61        32.88        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       60.30        50.66        16.93        44.75        39.32         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        38.79         4.04        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         0.39         7.96         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        0.39         3.39        37.58       133.25       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 
        1.94        60.53        36.39        68.38        71.18        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       40.21        38.66        39.12        33.11        27.91        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       11.77         9.73        14.20        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        4.44        10.65        13.91         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-7222 
        5.46         8.75        27.45        28.96        21.90        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
       14.53        31.27        30.41        19.76         0.10        17.49 
TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       33.24         4.93         3.48        26.89        14.07         1.35 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       19.23        13.32        18.74         0.26        14.47         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.25        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       85.12        34.36        35.24        29.92        21.11        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2714 TCGA-60-2716 
       10.22        96.82        37.94        49.48        50.33        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       42.64         3.19        35.90        23.57        26.83        11.77 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG 
       52.67        70.13        70.42        68.15       102.67        70.62 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       58.65        59.97        45.57        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2737 
       89.29        78.28        36.16        53.88        16.96         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 
       21.07         0.99         1.02         2.01         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         7.07        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 
       19.00         3.98        12.00        24.95        25.97        40.01 
TCGA-66-2788 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
       22.98        22.98        30.02        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        2.73         6.64         6.94        16.18        14.73        12.07 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 
       29.56        73.12        75.09        23.28        11.18         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       73.22        70.13       106.95         0.16        46.78        32.55 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        6.51        86.76        55.73        37.81       156.66        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       53.92        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       27.39         6.97        54.41        36.36       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH 
      150.25        22.29         5.92        61.94        27.62        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
        9.67        41.39         6.41        36.53        34.95        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1.38         1.15        29.95        25.15        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
       31.56        26.79        30.64        10.09         0.76        22.45 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
       16.77         3.09        32.71        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       38.14        12.59        18.08        22.59        30.28        34.13 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       30.97        19.86        24.36        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       16.21        15.85        14.96        15.29        29.92        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
        3.65        24.92         2.93        11.77        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
       10.59         2.70         3.48         5.26         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        5.03        26.63        14.14        17.69        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44        30.81        30.67        21.34 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
       18.15         2.01        27.02        20.32        18.58        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH 
       12.89        16.11        13.18        11.84         4.54         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       13.74         4.21        49.28        43.92        25.32        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V 
       26.43        83.57         3.65        33.07         3.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.30              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           140.09            173.82 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           21.370            21.945 
[1] "0.3 - 140.1 (21.4)" "0.0 - 173.8 (21.9)"
[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       23        0        12        10
  5P LOSS WILD-TYPE       2       72      129        2        53        85
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  5P LOSS MUTATED           1         11          5        0
  5P LOSS WILD-TYPE         2         52         14        7
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                17                72
  STAGE IB                23               129
  STAGE II                 0                 2
  STAGE IIA               12                53
  STAGE IIB               10                85
  STAGE III                1                 2
  STAGE IIIA              11                52
  STAGE IIIB               5                14
  STAGE IV                 0                 7
[1] 10  2
[1] 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    24  40  11   4
  5P LOSS WILD-TYPE  88 254  60  20
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              24                88
  T2              40               254
  T3              11                60
  T4               4                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                 N0  N1  N2  N3
  5P LOSS MUTATED    49  18   8   2
  5P LOSS WILD-TYPE 268 115  32   3
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              49               268
  N1              18               115
  N2               8                32
  N3               2                 3
[1] 4 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    65   0
  5P LOSS WILD-TYPE 346   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     65    0
  5P LOSS WILD-TYPE  346    7
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              65               346
  1               0                 7
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    16  63
  5P LOSS WILD-TYPE 114 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     16   63
  5P LOSS WILD-TYPE  114  308
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              16               114
  MALE                63               308
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    58  11
  5P LOSS WILD-TYPE 326  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     58   11
  5P LOSS WILD-TYPE  326   42
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               58               326
  YES              11                42
[1] 2 2
[1] FALSE
D50V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED                                       4
  5P LOSS WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  5P LOSS MUTATED                                        1
  5P LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED                                         0
  5P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                            74
  5P LOSS WILD-TYPE                                                         405
D50V10, multiclass
                                                             clus
vv                                                            5P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              74
                                                             clus
vv                                                            5P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               405
[1] 4 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    58   3   0   7
  5P LOSS WILD-TYPE 341   9   4  16
D50V13, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              58               341
  R1               3                 9
  R2               0                 4
  RX               7                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       1                         4    57
  5P LOSS WILD-TYPE     8                        27   292
D50V14, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               4                27
  WHITE                                  57               292
[1] 3 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     3  47
  5P LOSS WILD-TYPE   5 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   47
  5P LOSS WILD-TYPE    5  270
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              47               270
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   169 116
  5Q LOSS WILD-TYPE 111  98
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              285               209 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              116                98 
$`5Q LOSS MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-22-5471 TCGA-22-5472 
      123.19         4.80        31.99         6.18        60.66        64.93 
TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      129.01       133.74        19.76        31.50        28.96        31.27 
TCGA-43-2578 TCGA-43-5668 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 TCGA-56-8305 
       22.49        18.38         2.93        11.61        19.99         3.45 
TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       17.00        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2721 TCGA-68-8250 TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       32.32         8.02         9.50        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-NC-A5HD 
       18.38        16.14        57.07        19.36         5.69         0.07 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 
       39.85        40.90        65.65        16.80         8.58        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-4086 
      117.57        11.34        23.54        92.15        36.07         2.79 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 TCGA-21-1079 TCGA-21-1082 TCGA-21-5784 
      154.32       119.54        99.16        31.73       119.80        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 
       33.93        10.82        21.99         7.33         4.31         1.74 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       20.48        35.08        38.17        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
       19.30         9.57        63.55        14.63        44.25        86.30 
TCGA-22-5485 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-4587 
       30.12        56.32        97.94        79.53        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       63.35         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 
       44.19       118.36        61.61        32.88        65.23        60.30 
TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       44.75         4.96         1.12        38.79         4.04        26.43 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-A5EL TCGA-37-A5EN 
        8.12         7.46         7.82         6.81        37.58        21.70 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 TCGA-39-5036 
      133.25       126.58        82.52       102.18         1.94        71.18 
TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6647 
       55.56        40.21        38.66        39.12        27.91        24.89 
TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 
       21.47         3.81        19.59        11.77        14.20        13.32 
TCGA-46-3766 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       12.16         9.83         4.44        10.65        13.91         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-5897 
       29.95        28.34         5.46        30.35         8.75        12.43 
TCGA-56-5898 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
       18.25        31.27        19.76         6.51         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8304 TCGA-56-8309 TCGA-56-8622 TCGA-56-8625 
       33.24        14.96         3.48        14.07         1.81        10.36 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
       20.25        15.81        20.94        13.32        18.74         0.26 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J 
       13.25        13.55        29.95        71.24        16.47        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-60-2695 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       34.36        56.65        21.11        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2720 TCGA-60-2722 
       49.48        66.54        56.91        50.33         3.19        29.85 
TCGA-60-2723 TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       35.90        52.67        70.13        68.15        55.30       102.67 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW 
       59.97        45.57        25.28        78.28        16.37        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
       34.59        16.96        43.10         2.01        21.07         1.02 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 
        0.92         0.99        43.99        25.05         0.99         1.02 
TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        7.07         3.02         2.01        12.03         3.98        12.00 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 
        1.97        40.01        22.98         4.04         5.03        10.06 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
       54.08        49.05         2.73         6.64         6.94        13.35 
TCGA-70-6723 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-8007 
       12.33       140.09         0.49        73.22         0.16         6.51 
TCGA-77-8128 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       37.81        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G8 
        6.97        66.51        65.49        60.53       150.25        61.94 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 
       38.86        41.39        40.24         6.41        34.95        31.30 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
        1.38         1.15        18.94        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
       30.64        34.52        10.09         0.76        13.22        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
        5.29         3.09        32.71         2.01         7.76        36.59 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A511 
       22.59        34.13        30.97        19.86        19.73        14.96 
TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-92-8063 TCGA-92-8064 
       15.29         3.65         2.93        22.62         4.01         5.26 
TCGA-94-8035 TCGA-94-8490 TCGA-96-7544 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
        4.01         5.03        71.01        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW 
       27.16        18.15         2.01        12.89        16.11        13.41 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54        64.54        57.30        13.74         4.21         2.89 
TCGA-NC-A5HP TCGA-NK-A5CX TCGA-O2-A52S 
       25.32         3.65        12.72 

$`5Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 
       12.20         4.47        27.19        32.19        14.93        48.82 
TCGA-22-A5C4 TCGA-33-4589 TCGA-39-5039 TCGA-43-7657 TCGA-43-7658 TCGA-43-A56V 
       22.06         1.55        17.88         7.76        78.18        12.03 
TCGA-56-8201 TCGA-56-8504 TCGA-60-2712 TCGA-60-2715 TCGA-63-A5MH TCGA-77-7140 
       13.05        16.77         9.01        35.34        66.61        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE 
       42.08        30.81         2.76        21.21        19.10        76.80 
TCGA-NK-A7XE TCGA-18-3419 TCGA-18-3421 TCGA-18-5592 TCGA-21-1071 TCGA-21-1075 
        0.43        92.42        86.96        49.94        46.88        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
       60.89        34.78        15.58       122.43         9.34        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 
       31.63        88.11        64.21        14.10        27.02        48.33 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
       24.13         0.56        11.77         0.79        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5492 TCGA-33-4566 TCGA-33-4582 
       11.74        18.84        62.86        16.64       173.82       103.53 
TCGA-33-4583 TCGA-33-AASL TCGA-34-2596 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
      151.27        27.16         2.63        81.24        74.66         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       50.66        16.93        39.32        33.90         4.01         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 
        0.39         7.96         0.39         3.39       111.35        68.58 
TCGA-39-5022 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
       55.20         1.71        24.33        60.53        36.39        68.38 
TCGA-39-5040 TCGA-43-3920 TCGA-43-6143 TCGA-43-6771 TCGA-43-8115 TCGA-43-A475 
       17.06        33.11        22.98         5.46        13.38         9.73 
TCGA-46-3767 TCGA-51-4080 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-7222 
       13.02         0.39        27.45        28.96        21.90        18.48 
TCGA-56-7223 TCGA-56-7580 TCGA-56-8083 TCGA-56-8307 TCGA-56-8503 TCGA-56-8623 
       14.53        30.41         4.93        26.89         1.35        22.75 
TCGA-56-8624 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A62T TCGA-58-8386 TCGA-58-8393 
       13.81         9.93        19.23        14.47         0.03        34.78 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       35.24        29.92        12.23        10.22        96.82        37.94 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7021 
       48.49        42.64        23.57        26.83        11.77        70.42 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MV 
       70.62        58.65        14.99        11.34        89.29        36.16 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2758 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 
        0.99         2.01        21.01         2.01         2.01         2.01 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 TCGA-66-2783 TCGA-66-2786 TCGA-66-2790 
       23.01        19.00        19.00        24.95        25.97        22.98 
TCGA-66-2792 TCGA-66-2795 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 
       30.02         4.01        16.18        14.73        12.07        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 
       73.12        75.09        23.28        11.18        70.13       106.95 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 
       46.78        32.55        86.76        55.73       156.66        12.59 
TCGA-77-8133 TCGA-77-8144 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       53.92        27.39        54.41        36.36       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-6175 TCGA-85-7696 TCGA-85-7699 
       22.29         5.92        27.62         9.67        36.53        32.91 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8350 TCGA-85-8479 TCGA-85-8582 
       29.95        25.15        19.04        22.45        15.39        38.14 
TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       12.59        18.08        30.28        24.36        30.48        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 
       16.21        15.85        29.92        12.39        24.92        11.77 
TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8065 TCGA-94-8491 
       20.22        10.59         2.70         3.48         2.30        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       14.14        17.69        18.31        17.46        27.68        21.44 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-LA-A446 TCGA-MF-A522 
       27.02        20.32        18.58        20.71        13.18        11.84 
TCGA-NC-A5HH TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
        1.22        49.28        43.92        14.73        26.43        83.57 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         3.72        43.89        11.18         0.20 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.07              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           154.32            173.82 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            21.04             22.98 
[1] "0.1 - 154.3 (21.0)" "0.0 - 173.8 (23.0)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         1       50       92        1        39        48
  5Q LOSS WILD-TYPE       1       39       60        1        26        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  5Q LOSS MUTATED           1         38         11        6
  5Q LOSS WILD-TYPE         2         25          8        1
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                50                39
  STAGE IB                92                60
  STAGE II                 1                 1
  STAGE IIA               39                26
  STAGE IIB               48                47
  STAGE III                1                 2
  STAGE IIIA              38                25
  STAGE IIIB              11                 8
  STAGE IV                 6                 1
[1] 10  2
[1] 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    65 171  37  17
  5Q LOSS WILD-TYPE  47 123  34   7
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              65                47
  T2             171               123
  T3              37                34
  T4              17                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q LOSS MUTATED   193  70  23   2
  5Q LOSS WILD-TYPE 124  63  17   3
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0             193               124
  N1              70                63
  N2              23                17
  N3               2                 3
[1] 4 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   232   6
  5Q LOSS WILD-TYPE 179   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    232    6
  5Q LOSS WILD-TYPE  179    1
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0             232               179
  1               6                 1
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    73 217
  5Q LOSS WILD-TYPE  57 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     73  217
  5Q LOSS WILD-TYPE   57  154
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              73                57
  MALE               217               154
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   217  34
  5Q LOSS WILD-TYPE 167  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    217   34
  5Q LOSS WILD-TYPE  167   19
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO              217               167
  YES              34                19
[1] 2 2
[1] FALSE
D51V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                      10
  5Q LOSS WILD-TYPE                                     5
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  5Q LOSS MUTATED                                        2
  5Q LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                         1
  5Q LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                           277
  5Q LOSS WILD-TYPE                                                         202
D51V10, multiclass
                                                             clus
vv                                                            5Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             277
                                                             clus
vv                                                            5Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               202
[1] 4 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   227   8   2  15
  5Q LOSS WILD-TYPE 172   4   2   8
D51V13, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0             227               172
  R1               8                 4
  R2               2                 2
  RX              15                 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                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       3                        21   204
  5Q LOSS WILD-TYPE     6                        10   145
D51V14, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              21                10
  WHITE                                 204               145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5 187
  5Q LOSS WILD-TYPE   3 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5  187
  5Q LOSS WILD-TYPE    3  130
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             187               130
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    58  55
  6P LOSS WILD-TYPE 222 159
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              113               381 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               55               159 
$`6P LOSS MUTATED`
TCGA-18-3416 TCGA-18-4083 TCGA-34-2604 TCGA-39-5039 TCGA-43-8118 TCGA-43-A474 
       31.99         6.18        31.50        17.88         2.93        11.61 
TCGA-43-A56V TCGA-94-A5I4 TCGA-96-A4JK TCGA-J1-A4AH TCGA-NK-A5D1 TCGA-18-3408 
       12.03        16.14        19.36        19.10        16.80        75.75 
TCGA-18-3412 TCGA-18-3415 TCGA-18-4721 TCGA-18-5592 TCGA-21-1076 TCGA-21-5783 
       11.34        92.15       154.32        49.94        60.89        88.11 
TCGA-22-0940 TCGA-22-1012 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4609 
       21.99        14.10        24.13         0.56        38.17         9.57 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5483 TCGA-22-5492 
       63.55        44.25         0.79        86.30        18.84        16.64 
TCGA-33-4547 TCGA-33-4583 TCGA-33-AASD TCGA-33-AASL TCGA-34-2596 TCGA-34-8455 
       79.53       151.27       110.99        27.16         2.63         4.04 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 TCGA-39-5034 TCGA-39-5037 
        3.39       126.58        68.58       102.18        36.39        55.56 
TCGA-43-6143 TCGA-43-8115 TCGA-43-A475 TCGA-46-3765 TCGA-46-3768 TCGA-46-6025 
       22.98        13.38         9.73        13.32         9.83        10.65 
TCGA-51-4081 TCGA-52-7622 TCGA-56-7579 TCGA-56-7582 TCGA-56-7822 TCGA-56-8624 
       29.95        28.34        31.27        19.76        17.49        13.81 
TCGA-56-A4ZK TCGA-58-8386 TCGA-60-2698 TCGA-60-2707 TCGA-60-2722 TCGA-60-2723 
       18.74         0.03        10.22        21.93        29.85        35.90 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-A5MJ TCGA-63-A5MR TCGA-66-2758 
       11.77        70.13        70.42        59.97        89.29        21.01 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 TCGA-66-2789 TCGA-66-2792 TCGA-66-2794 
       12.03        12.00        25.97         4.04        30.02        54.08 
TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I TCGA-70-6723 TCGA-77-8007 TCGA-77-8009 
        2.73         6.64        16.18        12.33         6.51        55.73 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8140 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5G8 
       37.81        12.59        11.54        54.41       150.25        61.94 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7950 TCGA-85-8049 TCGA-85-8070 TCGA-85-8277 
       36.53        31.30        18.94        19.04        31.56        10.09 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A510 TCGA-85-A512 
       22.59        34.13        19.86        30.48        15.85        15.29 
TCGA-85-A5B5 TCGA-90-7767 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-96-7544 
        3.65         2.93         3.48         5.26         2.30        71.01 
TCGA-98-A53I TCGA-98-A53J TCGA-NC-A5HH TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HQ 
       18.58        20.71         1.22         2.89        49.28        14.73 
TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
       83.57        33.07         3.72        43.89         0.20 

$`6P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-21-A5DI 
       12.20         4.47       123.19         4.80        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       14.93        48.82        60.66        64.93        22.06       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 
      133.74         1.55        19.76        28.96        31.27        22.49 
TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
       18.38         7.76        78.18        19.99        13.05         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       17.00        16.77        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 
       41.42         9.01        35.34        32.32        66.61         8.02 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
       20.78        42.08        30.81         9.50        14.07        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D 
        0.16        18.38        57.07         2.76         5.69        21.21 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A7XE 
        0.07        76.80        39.85        40.90        65.65         0.43 
TCGA-O2-A52W TCGA-18-3411 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
        8.58       117.57        23.54        36.07        92.42        86.96 
TCGA-18-4086 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 
        2.79       119.54        46.88        99.16        70.16        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       15.58        31.73       122.43         9.34       119.80        43.23 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 
       31.63        41.69        33.93        10.82         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
       64.21         1.74        27.02        20.48        35.08        48.33 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5474 
       34.75        13.12        32.02        19.30        11.77        14.63 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       71.34        79.20        11.74        30.12        62.86        56.32 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
       97.94       173.82       103.53        14.07        54.44        63.35 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ 
        4.70         0.30        36.62         6.94        44.19       118.36 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       61.61        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       60.30        50.66        16.93        44.75        39.32         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        1.12        38.79        26.43        33.90         4.01         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.39         7.96         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 TCGA-39-5022 
        0.39        37.58        21.70       133.25       111.35        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 
       82.52         1.71        24.33         1.94        60.53        68.38 
TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       71.18        17.06        40.21        38.66        39.12        33.11 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6026 
       11.77        14.20        12.16        13.02         4.44        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
        0.39         0.39         5.46        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 
       28.96        12.43        18.25        21.90        18.48        14.53 
TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
       30.41         6.51         0.10        33.24        14.96         4.93 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        3.48        26.89        14.07         1.35         1.81        22.75 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
       10.36         9.93        20.25        15.81        20.94        19.23 
TCGA-56-A4BX TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       13.32         0.26        14.47        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       71.24        16.47        34.78        85.12        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       35.24        29.92        21.11        12.23        96.82        37.94 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       92.71        80.45        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 
       48.49        42.64         3.19        23.57        26.83        52.67 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5ML 
       68.15        55.30       102.67        70.62        58.65        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       14.99        11.34        25.28        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       53.88        34.59        16.96        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        0.99         1.02         2.01         0.92         0.99        43.99 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       25.05         0.99         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        7.07        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 
        3.98        24.95         1.97        40.01        22.98        22.98 
TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 TCGA-68-8251 
        5.03        10.06         4.01        49.05         6.94        13.35 
TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       14.73        12.07        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       11.18       140.09         0.49        73.22        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8130 TCGA-77-8133 
        0.16        46.78        32.55        86.76       156.66        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       39.09        17.72       104.09        26.40        27.39         6.97 
TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       66.51        65.49        60.53        36.36       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       22.29         5.92        27.62        38.86         9.67        41.39 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       40.24         6.41        34.95        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       29.95        25.15        24.13        26.79        30.64        34.52 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
        0.76        13.22        22.45        16.77         5.29         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       32.71         2.01        15.39         7.76        36.59        38.14 
TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR 
       12.59        18.08        30.28        30.97        24.36        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       27.16        16.21        14.96        29.92        12.39        24.92 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
       11.77        20.22        22.62        10.59         2.70         4.01 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 
        4.01         5.03        26.63        14.14        17.69        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 
       27.16        18.15         2.01        27.02        20.32        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG 
       16.11        13.18        13.41        11.84         4.54        64.54 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT 
       57.30        13.74         4.21        43.92        25.32        26.43 
TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A5IB 
        3.65        12.72        11.18 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.03              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           154.32            173.82 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            19.76             22.45 
[1] "0.0 - 154.3 (19.8)" "0.1 - 173.8 (22.4)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         1       17       31        1        19        25
  6P LOSS WILD-TYPE       1       72      121        1        46        70
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  6P LOSS MUTATED           1         13          2        2
  6P LOSS WILD-TYPE         2         50         17        5
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                17                72
  STAGE IB                31               121
  STAGE II                 1                 1
  STAGE IIA               19                46
  STAGE IIB               25                70
  STAGE III                1                 2
  STAGE IIIA              13                50
  STAGE IIIB               2                17
  STAGE IV                 2                 5
[1] 10  2
[1] 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    24  67  20   3
  6P LOSS WILD-TYPE  88 227  51  21
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              24                88
  T2              67               227
  T3              20                51
  T4               3                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                 N0  N1  N2  N3
  6P LOSS MUTATED    65  39   7   1
  6P LOSS WILD-TYPE 252  94  33   4
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              65               252
  N1              39                94
  N2               7                33
  N3               1                 4
[1] 4 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    95   2
  6P LOSS WILD-TYPE 316   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     95    2
  6P LOSS WILD-TYPE  316    5
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              95               316
  1               2                 5
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    27  87
  6P LOSS WILD-TYPE 103 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     27   87
  6P LOSS WILD-TYPE  103  284
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              27               103
  MALE                87               284
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    90  12
  6P LOSS WILD-TYPE 294  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     90   12
  6P LOSS WILD-TYPE  294   41
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               90               294
  YES              12                41
[1] 2 2
[1] FALSE
D52V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED                                       4
  6P LOSS WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  6P LOSS MUTATED                                        1
  6P LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED                                         0
  6P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                           109
  6P LOSS WILD-TYPE                                                         370
D52V10, multiclass
                                                             clus
vv                                                            6P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             109
                                                             clus
vv                                                            6P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               370
[1] 4 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    93   2   0   8
  6P LOSS WILD-TYPE 306  10   4  15
D52V13, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              93               306
  R1               2                10
  R2               0                 4
  RX               8                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         7    78
  6P LOSS WILD-TYPE     8                        24   271
D52V14, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               7                24
  WHITE                                  78               271
[1] 3 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  72
  6P LOSS WILD-TYPE   6 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   72
  6P LOSS WILD-TYPE    6  245
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              72               245
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    60  52
  6Q LOSS WILD-TYPE 220 162
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              112               382 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               52               162 
$`6Q LOSS MUTATED`
TCGA-18-3416 TCGA-18-4083 TCGA-34-2604 TCGA-39-5039 TCGA-43-8118 TCGA-56-A4BY 
       31.99         6.18        31.50        17.88         2.93        17.85 
TCGA-96-A4JK TCGA-J1-A4AH TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3411 
       19.36        19.10        40.90        16.80        75.75       117.57 
TCGA-18-3412 TCGA-18-3415 TCGA-18-5592 TCGA-21-1076 TCGA-21-5783 TCGA-21-5787 
       11.34        92.15        49.94        60.89        88.11        10.82 
TCGA-22-0940 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 
       21.99        24.13         0.56        38.17        34.75        19.30 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5492 TCGA-33-4582 TCGA-33-4583 TCGA-33-AASD 
        0.79        86.30        16.64       103.53       151.27       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-5928 TCGA-34-8455 TCGA-37-5819 
       44.19        27.16         2.63        39.32         4.04         3.39 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 TCGA-39-5034 TCGA-39-5037 TCGA-43-2581 
      126.58        68.58       102.18        36.39        55.56        38.66 
TCGA-43-6143 TCGA-43-8115 TCGA-46-3765 TCGA-46-6025 TCGA-51-4081 TCGA-52-7622 
       22.98        13.38        13.32        10.65        29.95        28.34 
TCGA-52-7812 TCGA-56-7582 TCGA-56-7730 TCGA-56-8624 TCGA-56-8625 TCGA-56-A4ZK 
       27.45        19.76         6.51        13.81        10.36        18.74 
TCGA-58-8386 TCGA-58-A46M TCGA-60-2707 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 
        0.03        35.24        21.93        29.85        35.90        11.77 
TCGA-63-7020 TCGA-63-A5MR TCGA-66-2758 TCGA-66-2763 TCGA-66-2773 TCGA-66-2780 
       70.13        89.29        21.01         0.99         3.02        12.03 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2792 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
       12.00        24.95        30.02         4.01         2.73         6.64 
TCGA-68-A59I TCGA-70-6723 TCGA-77-7141 TCGA-77-8007 TCGA-77-8009 TCGA-77-8131 
       16.18        12.33         0.49         6.51        55.73        12.59 
TCGA-77-8140 TCGA-77-8150 TCGA-77-A5G8 TCGA-85-6560 TCGA-85-7696 TCGA-85-7698 
       11.54        54.41        61.94        41.39        36.53        31.30 
TCGA-85-7710 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8354 
        1.38        24.13        31.56        30.64        10.09        32.71 
TCGA-85-8479 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       15.39        19.86        30.48        19.73        27.16        16.21 
TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7767 TCGA-92-7341 TCGA-92-8065 TCGA-94-8491 
       15.85         3.65         2.93         3.48         2.30        26.63 
TCGA-96-7544 TCGA-98-A538 TCGA-98-A53I TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HN 
       71.01        27.16        18.58        64.54         1.22        49.28 
TCGA-NC-A5HQ TCGA-O2-A52N TCGA-O2-A52Q TCGA-XC-AA0X 
       14.73        33.07         3.72         0.20 

$`6Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-21-A5DI 
       12.20         4.47       123.19         4.80        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       14.93        48.82        60.66        64.93        22.06       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 
      133.74         1.55        19.76        28.96        31.27        22.49 
TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       18.38         7.76        78.18        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR 
       13.05         3.45        17.00        16.77        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
        3.58        41.42         9.01        35.34        32.32        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
        8.02        20.78        42.08        30.81         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-8020 
       21.04         0.16        18.38        16.14        57.07         2.76 
TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT 
        5.69        21.21         0.07        76.80        39.85        65.65 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
        0.43         8.58        23.54        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2.79       154.32       119.54        46.88        99.16        70.16 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       34.78        15.58        31.73       122.43         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1002 
       43.23        31.63        41.69        33.93         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       64.21         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       48.33        13.12        32.02         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       14.63        44.25        71.34        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       30.12        62.86        56.32        97.94        79.53       173.82 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       14.07        54.44        63.35         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASJ TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
        6.94       118.36        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        4.96         1.12        38.79        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         7.96         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 
        6.81         0.39        37.58        21.70       133.25       111.35 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       55.20        82.52         1.71        24.33         1.94        60.53 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 
       68.38        71.18        17.06        40.21        39.12        33.11 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       11.77         9.73        14.20        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 
        4.44        13.91         0.39         0.39         5.46        30.35 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
        8.75        28.96        12.43        18.25        21.90        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       14.53        31.27        30.41         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       14.96         4.93         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.81        22.75         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 
       19.23        13.32         0.26        14.47        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       56.65        29.92        21.11        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       37.94        92.71        80.45        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2724 TCGA-60-2725 
       50.33        48.49        42.64         3.19        23.57        26.83 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG 
       52.67        70.42        68.15        55.30       102.67        70.62 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       58.65        59.97        45.57        14.99        11.34        25.28 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        36.16        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       43.10         2.01        21.07         0.99         1.02         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
        0.92         0.99        43.99        25.05         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 
        2.01         2.01         7.07        23.01        19.00         2.01 
TCGA-66-2778 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
       19.00         3.98         1.97        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
        4.04        22.98         5.03        10.06        54.08        49.05 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 
        6.94        13.35        14.73        12.07        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 
       75.09        23.28        11.18       140.09        73.22        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8128 
      106.95         0.16        46.78        32.55        86.76        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 
      156.66        53.92        39.09        17.72       104.09        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
       27.39         6.97        66.51        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF 
      126.18       132.36       150.25        22.29         5.92        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 
       38.86         9.67        40.24         6.41        34.95        32.91 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 
        1.15        29.95        18.94        25.15        19.04        26.79 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       34.52         0.76        13.22        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        3.09         2.01         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA 
       18.08        22.59        30.28        34.13        30.97        24.36 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 
       14.96        15.29        29.92        12.39        24.92        11.77 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 
       20.22        22.62        10.59         2.70         4.01         5.26 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 
        4.01         5.03        14.14        17.69        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A 
       27.68        21.44        30.81        30.67        21.34        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 
        2.01        27.02        20.32        20.71        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HI TCGA-NC-A5HJ 
       13.18        13.41        11.84         4.54        57.30        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR 
        4.21         2.89        43.92        25.32        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
        3.65        12.72        43.89        11.18 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.03              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           151.27            173.82 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            21.47             21.80 
[1] "0.0 - 151.3 (21.5)" "0.1 - 173.8 (21.8)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         1       16       33        0        20        24
  6Q LOSS WILD-TYPE       1       73      119        2        45        71
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  6Q LOSS MUTATED           1         14          2        2
  6Q LOSS WILD-TYPE         2         49         17        5
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                16                73
  STAGE IB                33               119
  STAGE II                 0                 2
  STAGE IIA               20                45
  STAGE IIB               24                71
  STAGE III                1                 2
  STAGE IIIA              14                49
  STAGE IIIB               2                17
  STAGE IV                 2                 5
[1] 10  2
[1] 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    21  71  18   4
  6Q LOSS WILD-TYPE  91 223  53  20
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              21                91
  T2              71               223
  T3              18                53
  T4               4                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                 N0  N1  N2  N3
  6Q LOSS MUTATED    66  37   8   1
  6Q LOSS WILD-TYPE 251  96  32   4
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              66               251
  N1              37                96
  N2               8                32
  N3               1                 4
[1] 4 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    95   2
  6Q LOSS WILD-TYPE 316   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     95    2
  6Q LOSS WILD-TYPE  316    5
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              95               316
  1               2                 5
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    32  82
  6Q LOSS WILD-TYPE  98 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     32   82
  6Q LOSS WILD-TYPE   98  289
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              32                98
  MALE                82               289
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    85  15
  6Q LOSS WILD-TYPE 299  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     85   15
  6Q LOSS WILD-TYPE  299   38
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               85               299
  YES              15                38
[1] 2 2
[1] FALSE
D53V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED                                       6
  6Q LOSS WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  6Q LOSS MUTATED                                        2
  6Q LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED                                         0
  6Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                           106
  6Q LOSS WILD-TYPE                                                         373
D53V10, multiclass
                                                             clus
vv                                                            6Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             106
                                                             clus
vv                                                            6Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
D53V12, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    92   2   1   8
  6Q LOSS WILD-TYPE 307  10   3  15
D53V13, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              92               307
  R1               2                10
  R2               1                 3
  RX               8                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       2                         7    80
  6Q LOSS WILD-TYPE     7                        24   269
D53V14, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               7                24
  WHITE                                  80               269
[1] 3 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  72
  6Q LOSS WILD-TYPE   5 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   72
  6Q LOSS WILD-TYPE    5  245
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              72               245
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    37  22
  7P LOSS WILD-TYPE 243 192
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               59               435 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               22               192 
$`7P LOSS MUTATED`
TCGA-21-A5DI TCGA-43-2578 TCGA-56-8305 TCGA-60-2712 TCGA-94-A5I4 TCGA-J1-A4AH 
       32.19        22.49         3.45         9.01        16.14        19.10 
TCGA-18-3419 TCGA-21-1077 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-1016 
       92.42        34.78        43.23        33.93        10.82        27.02 
TCGA-22-4601 TCGA-22-5492 TCGA-33-6738 TCGA-33-AASJ TCGA-37-3789 TCGA-37-4133 
       34.75        16.64        63.35       118.36         0.43         7.82 
TCGA-37-5819 TCGA-39-5029 TCGA-39-5036 TCGA-43-6770 TCGA-46-6026 TCGA-56-1622 
        3.39        24.33        71.18        21.47        13.91        28.96 
TCGA-56-5898 TCGA-56-7580 TCGA-56-8082 TCGA-56-8629 TCGA-56-A4BW TCGA-58-8386 
       18.25        30.41        14.96        15.81        19.23         0.03 
TCGA-58-8390 TCGA-60-2695 TCGA-60-2703 TCGA-63-A5MS TCGA-66-2757 TCGA-66-2773 
       29.95        21.11        96.82        78.28        43.99         3.02 
TCGA-66-2783 TCGA-66-2788 TCGA-66-2792 TCGA-66-2793 TCGA-77-7142 TCGA-77-7337 
       24.95        22.98        30.02        10.06        73.22       106.95 
TCGA-77-8143 TCGA-77-8144 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-8070 
       26.40        27.39        38.86        41.39        32.91        31.56 
TCGA-85-8277 TCGA-85-8353 TCGA-85-A4JB TCGA-85-A510 TCGA-85-A512 TCGA-90-7767 
       10.09         3.09        30.97        15.85        15.29         2.93 
TCGA-98-A538 TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HT TCGA-O2-A5IB 
       27.16         4.21        43.92        26.43        11.18 

$`7P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       27.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
      129.01       133.74         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       31.27        17.88        18.38         7.76        78.18         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 
       11.61        12.03        19.99        13.05        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 
       17.85        21.04         0.13         3.58        41.42        35.34 
TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       32.32        66.61         8.02        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7545 
        9.50        14.07        21.04         0.16        18.38        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE 
       19.36         2.76         5.69        21.21         0.07        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
       39.85        40.90        65.65        16.80         0.43         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
       75.75       117.57        11.34        23.54        92.15        36.07 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       86.96         2.79       154.32        49.94       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       99.16        70.16        60.89        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 
        9.34       119.80        31.63        88.11        41.69        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 
        7.33         4.31        64.21         1.74        14.10        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
       35.08        48.33        24.13         0.56        38.17        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       32.02        19.30         9.57        11.77        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
       44.25         0.79        86.30        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 
       18.84        30.12        62.86        56.32        97.94        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN 
      173.82       103.53       151.27        14.07        54.44         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL 
        0.30        36.62         6.94       110.99        44.19        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        2.63        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        60.30        50.66        16.93        44.75        39.32 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
        4.96         1.12        38.79         4.04        26.43        33.90 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
        4.01         0.39         7.96         8.12         7.46         6.81 
TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        0.39        37.58        21.70       133.25       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
       68.58        55.20        82.52       102.18         1.71         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       60.53        36.39        68.38        55.56        17.06        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       38.66        39.12        33.11        27.91        22.98        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
        5.46         3.81        19.59        13.38        11.77         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       14.20        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 
       30.35         8.75        27.45        12.43        21.90        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
       14.53        31.27        19.76         6.51         0.10        17.49 
TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       33.24         4.93         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75        13.81        10.36         9.93        20.25 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 
       20.94        13.32        18.74         0.26        14.47        13.25 
TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       13.55        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 
       56.65        35.24        29.92        12.23        10.22        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       92.71        21.93        80.45        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       50.33        48.49        42.64         3.19        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
       23.57        26.83        11.77        52.67        70.13        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       68.15        55.30       102.67        70.62        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT 
       45.57        14.99        11.34        25.28        89.29        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
       36.16        53.88        34.59        16.96        43.10         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       21.07         0.99         1.02         2.01         0.92         0.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 
        2.01         7.07        23.01        19.00         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
       12.03         3.98        12.00         1.97        25.97        40.01 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        4.04        22.98         5.03        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         6.94        13.35        16.18        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 
       11.18       140.09         0.49        70.13         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       32.55         6.51        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       12.59        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97        66.51        54.41        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       150.25        22.29         5.92        61.94 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       27.62         9.67        40.24         6.41        36.53        34.95 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       31.30         1.38         1.15        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
       19.04        24.13        26.79        30.64        34.52         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
       13.22        22.45        16.77         5.29        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
       15.39         7.76        36.59        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       22.59        30.28        34.13        19.86        24.36        30.48 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       19.73        27.16        16.21        14.96        29.92        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        3.65        24.92        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
        2.70         3.48         4.01         5.26         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        5.03        26.63        14.14        17.69        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44        30.81        30.67        21.34 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
       18.15         2.01        27.02        20.32        18.58        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       12.89        16.11        13.18        13.41        11.84         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN 
       64.54         1.22        57.30        13.74         2.89        49.28 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q 
       25.32        14.73        83.57         3.65        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       12.72        43.89         0.20 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.03              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           118.36            173.82 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            24.95             21.21 
[1] "0.0 - 118.4 (24.9)" "0.1 - 173.8 (21.2)"
[1] "hr=" "1.1"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0        5       17        0         9        12
  7P LOSS WILD-TYPE       2       84      135        2        56        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  7P LOSS MUTATED           1         13          2        1
  7P LOSS WILD-TYPE         2         50         17        6
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 5                84
  STAGE IB                17               135
  STAGE II                 0                 2
  STAGE IIA                9                56
  STAGE IIB               12                83
  STAGE III                1                 2
  STAGE IIIA              13                50
  STAGE IIIB               2                17
  STAGE IV                 1                 6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED     9  38   9   4
  7P LOSS WILD-TYPE 103 256  62  20
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               9               103
  T2              38               256
  T3               9                62
  T4               4                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                 N0  N1  N2  N3
  7P LOSS MUTATED    33  19   6   1
  7P LOSS WILD-TYPE 284 114  34   4
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              33               284
  N1              19               114
  N2               6                34
  N3               1                 4
[1] 4 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    48   1
  7P LOSS WILD-TYPE 363   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     48    1
  7P LOSS WILD-TYPE  363    6
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              48               363
  1               1                 6
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    13  47
  7P LOSS WILD-TYPE 117 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     13   47
  7P LOSS WILD-TYPE  117  324
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE              13               117
  MALE                47               324
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    45   5
  7P LOSS WILD-TYPE 339  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     45    5
  7P LOSS WILD-TYPE  339   48
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               45               339
  YES               5                48
[1] 2 2
[1] FALSE
D54V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                       1
  7P LOSS WILD-TYPE                                    14
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  7P LOSS MUTATED                                        0
  7P LOSS WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                         0
  7P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                            59
  7P LOSS WILD-TYPE                                                         420
D54V10, multiclass
                                                             clus
vv                                                            7P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              59
                                                             clus
vv                                                            7P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               420
[1] 4 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    52   0   2   2
  7P LOSS WILD-TYPE 347  12   2  21
D54V13, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              52               347
  R1               0                12
  R2               2                 2
  RX               2                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       0                         3    44
  7P LOSS WILD-TYPE     9                        28   305
D54V14, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               3                28
  WHITE                                  44               305
[1] 3 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  38
  7P LOSS WILD-TYPE   7 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   38
  7P LOSS WILD-TYPE    7  279
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              38               279
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    30  18
  7Q LOSS WILD-TYPE 250 196
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               48               446 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               18               196 
$`7Q LOSS MUTATED`
TCGA-43-2578 TCGA-56-8305 TCGA-60-2712 TCGA-63-A5MH TCGA-77-A5GB TCGA-94-A5I4 
       22.49         3.45         9.01        66.61        30.81        16.14 
TCGA-J1-A4AH TCGA-NC-A5HM TCGA-18-3419 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 
       19.10        39.85        92.42       119.80        43.23        33.93 
TCGA-22-1016 TCGA-22-5481 TCGA-22-5482 TCGA-37-3789 TCGA-37-5819 TCGA-39-5029 
       27.02        79.20        11.74         0.43         3.39        24.33 
TCGA-43-2581 TCGA-43-6770 TCGA-43-6771 TCGA-46-3765 TCGA-46-6026 TCGA-56-1622 
       38.66        21.47         5.46        13.32        13.91        28.96 
TCGA-56-7580 TCGA-56-8629 TCGA-56-A4BW TCGA-60-2695 TCGA-60-2703 TCGA-63-A5MS 
       30.41        15.81        19.23        21.11        96.82        78.28 
TCGA-66-2754 TCGA-66-2773 TCGA-66-2788 TCGA-66-2793 TCGA-77-7138 TCGA-77-8136 
        2.01         3.02        22.98        10.06        11.18        39.09 
TCGA-77-8139 TCGA-77-8144 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-8048 
      104.09        27.39        38.86        41.39        32.91        25.15 
TCGA-85-8353 TCGA-85-A4JB TCGA-85-A510 TCGA-90-7767 TCGA-98-8022 TCGA-NC-A5HK 
        3.09        30.97        15.85         2.93        30.67         4.21 

$`7Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 
       27.19        32.19        14.93        48.82        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       22.06       129.01       133.74         1.55        19.76        31.50 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       28.96        31.27        17.88        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 
        2.93        11.61        12.03        19.99        13.05        17.00 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       16.77        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 
       35.34        32.32         8.02        20.78        42.08         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JK 
       14.07        21.04         0.16        18.38        57.07        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HR 
        2.76         5.69        21.21         0.07        76.80        40.90 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       65.65        16.80         0.43         8.58        75.75       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 
       11.34        23.54        92.15        36.07        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      154.32        49.94       119.54        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       60.89        34.78        15.58        31.73       122.43         9.34 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
       31.63        88.11        41.69        10.82        21.99         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
        4.31        64.21         1.74        14.10        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       48.33        24.13         0.56        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       32.02        19.30         9.57        11.77        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 
       44.25         0.79        86.30        71.34        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        56.32        16.64        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        0.30        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       39.32         4.96         1.12        38.79         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       33.90         4.01         0.39         7.96         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        7.82         6.81         0.39        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
        1.71         1.94        60.53        36.39        68.38        71.18 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       55.56        17.06        40.21        39.12        33.11        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       22.98        24.89         3.81        19.59        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
        9.73        14.20        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
       30.35         8.75        27.45        12.43        18.25        21.90 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       18.48        14.53        31.27        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       17.49        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
        9.93        20.25        20.94        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
       14.47         0.03        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       16.47        34.78        85.12        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       29.92        12.23        10.22        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       80.45        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       11.34        25.28        89.29        16.37        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       34.59        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        1.02         0.92         0.99        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
        0.99         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       23.01        19.00         2.01        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 
       12.00        24.95         1.97        25.97        40.01         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
       22.98         5.03        30.02        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         6.94        13.35        16.18        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        29.56        73.12        75.09        23.28 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
       46.78        32.55         6.51        86.76        55.73        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 
      156.66        12.59        53.92        17.72        11.54        26.40 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97        66.51        54.41        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       150.25        22.29         5.92        61.94 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       27.62         9.67        40.24         6.41        36.53        34.95 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
       31.30         1.38         1.15        29.95        18.94        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       24.13        31.56        26.79        30.64        34.52        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
        0.76        13.22        22.45        16.77         5.29        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01        15.39         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA 
       18.08        22.59        30.28        34.13        19.86        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
       30.48        19.73        27.16        16.21        14.96        15.29 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED 
       29.92        12.39         3.65        24.92        11.77        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       22.62        10.59         2.70         3.48         4.01         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        2.30         4.01         5.03        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       71.01        18.31        17.46        27.68        21.44        30.81 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       21.34        27.16        18.15         2.01        27.02        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       18.58        20.71        12.89        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       11.84         4.54        64.54         1.22        57.30        13.74 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
        2.89        49.28        43.92        25.32        14.73        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       83.57         3.65        33.07         3.72        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.43              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           119.80            173.82 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           23.655            21.390 
[1] "0.4 - 119.8 (23.7)" "0.0 - 173.8 (21.4)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         0        6       19        0         6        12
  7Q LOSS WILD-TYPE       2       83      133        2        59        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  7Q LOSS MUTATED           0          6          1        0
  7Q LOSS WILD-TYPE         3         57         18        7
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 6                83
  STAGE IB                19               133
  STAGE II                 0                 2
  STAGE IIA                6                59
  STAGE IIB               12                83
  STAGE III                0                 3
  STAGE IIIA               6                57
  STAGE IIIB               1                18
  STAGE IV                 0                 7
[1] 10  2
[1] 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     8  35   5   2
  7Q LOSS WILD-TYPE 104 259  66  22
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               8               104
  T2              35               259
  T3               5                66
  T4               2                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                 N0  N1  N2  N3
  7Q LOSS MUTATED    31  15   3   0
  7Q LOSS WILD-TYPE 286 118  37   5
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              31               286
  N1              15               118
  N2               3                37
  N3               0                 5
[1] 4 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    42   0
  7Q LOSS WILD-TYPE 369   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     42    0
  7Q LOSS WILD-TYPE  369    7
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              42               369
  1               0                 7
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    11  39
  7Q LOSS WILD-TYPE 119 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11   39
  7Q LOSS WILD-TYPE  119  332
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              11               119
  MALE                39               332
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    40   1
  7Q LOSS WILD-TYPE 344  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     40    1
  7Q LOSS WILD-TYPE  344   52
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               40               344
  YES               1                52
[1] 2 2
[1] FALSE
D55V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                       1
  7Q LOSS WILD-TYPE                                    14
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  7Q LOSS MUTATED                                        0
  7Q LOSS WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                         0
  7Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                            49
  7Q LOSS WILD-TYPE                                                         430
D55V10, multiclass
                                                             clus
vv                                                            7Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              49
                                                             clus
vv                                                            7Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               430
[1] 4 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    44   0   1   4
  7Q LOSS WILD-TYPE 355  12   3  19
D55V13, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              44               355
  R1               0                12
  R2               1                 3
  RX               4                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         1    35
  7Q LOSS WILD-TYPE     9                        30   314
D55V14, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               1                30
  WHITE                                  35               314
[1] 3 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  30
  7Q LOSS WILD-TYPE   7 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   30
  7Q LOSS WILD-TYPE    7  287
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              30               287
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   133 105
  8P LOSS WILD-TYPE 147 109
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              238               256 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              105               109 
$`8P LOSS MUTATED`
TCGA-18-3406 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 
       12.20         6.18        27.19        14.93        48.82        60.66 
TCGA-33-4589 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-8118 
        1.55        31.27        17.88        18.38         7.76         2.93 
TCGA-43-A474 TCGA-56-8201 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2711 
       11.61        13.05        16.77        17.85         0.13        41.42 
TCGA-60-2721 TCGA-77-A5GA TCGA-90-7766 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK 
       32.32        42.08         9.50         0.16        16.14        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
        2.76         5.69        19.10        76.80        39.85        40.90 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3419 TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 
       11.34        92.15        92.42       154.32        49.94        99.16 
TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 
       60.89       122.43        43.23        31.63        33.93        10.82 
TCGA-22-1002 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4599 TCGA-22-4601 
        4.31        27.02        20.48        48.33        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5477 TCGA-22-5478 
       13.12        32.02         9.57        11.77        44.25         0.79 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
       71.34        79.20        18.84        30.12        56.32        16.64 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN 
       79.53       173.82       103.53        14.07        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 
        0.30        36.62       110.99        44.19        27.16         2.63 
TCGA-34-2600 TCGA-34-5236 TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 
       61.61         9.07        16.93        39.32        38.79         4.04 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EN 
        4.01         0.43         0.39         6.81         0.39        21.70 
TCGA-39-5011 TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 TCGA-39-5037 TCGA-43-2576 
      133.25        68.58       102.18        60.53        55.56        40.21 
TCGA-43-2581 TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-8116 TCGA-46-3765 
       38.66        21.47         5.46        13.38        11.77        13.32 
TCGA-46-3766 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-51-4080 TCGA-51-4081 
       12.16         9.83         4.44        10.65         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
       28.34         5.46        30.35        27.45        28.96        12.43 
TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-8082 
       18.25        18.48        14.53        31.27        30.41        14.96 
TCGA-56-8083 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
        4.93         9.93        20.25        15.81        19.23        13.32 
TCGA-56-A5DS TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L 
        0.26        29.95        16.47        34.78        34.36        56.65 
TCGA-58-A46M TCGA-60-2698 TCGA-60-2703 TCGA-60-2713 TCGA-60-2723 TCGA-60-2726 
       35.24        10.22        96.82        56.91        35.90        11.77 
TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT 
       59.97        14.99        11.34        25.28        78.28        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2753 
       36.16        53.88        16.96        43.10         2.01         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2766 TCGA-66-2768 
        2.01         0.92        43.99        25.05         1.02         2.01 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
       12.03         3.98        12.00        24.95         1.97        40.01 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7755 TCGA-68-A59I 
       22.98         5.03        30.02         4.01         2.73        16.18 
TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 
       14.73        12.07        12.33        29.56        75.09        23.28 
TCGA-77-7138 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
       11.18       106.95         0.16        32.55        86.76        55.73 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       37.81       156.66       104.09        27.39         6.97        66.51 
TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 
       60.53       150.25        22.29        61.94        27.62         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
       40.24         6.41        36.53        34.95        31.30         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8070 TCGA-85-8276 
        1.15        29.95        18.94        25.15        31.56        34.52 
TCGA-85-8277 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8582 
       10.09        22.45         5.29         3.09        32.71        38.14 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       34.13        30.97        19.86        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED 
       16.21        14.96        12.39         3.65         2.93        20.22 
TCGA-92-7341 TCGA-92-8063 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        3.48         4.01        26.63        14.14        17.69        71.01 
TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53J TCGA-LA-A446 
       17.46        30.81        30.67        27.16        20.71        13.18 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HP 
       11.84        64.54        57.30        13.74         2.89        25.32 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-O2-A52S TCGA-O2-A52V 
       14.73        26.43        12.72        43.89 

$`8P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-21-A5DI TCGA-22-5472 
        4.47       123.19         4.80        31.99        32.19        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
       22.06       129.01       133.74        19.76        31.50        28.96 
TCGA-43-2578 TCGA-43-7658 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 TCGA-56-8308 
       22.49        78.18        12.03        19.99         3.45        17.00 
TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2712 TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 
       21.04         3.58         9.01        35.34        66.61         8.02 
TCGA-77-7140 TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 
       20.78        30.81        14.07        21.04        18.38        57.07 
TCGA-98-A53D TCGA-NC-A5HD TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
       21.21         0.07        65.65        16.80         0.43         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 
       75.75       117.57        23.54        36.07        86.96         2.79 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
      119.54        46.88        70.16        34.78        15.58        31.73 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 
        9.34       119.80        88.11        41.69        21.99         7.33 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 
       64.21         1.74        14.10        35.08        24.13         0.56 
TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5489 
       19.30        63.55        14.63        86.30        11.74        62.86 
TCGA-33-4538 TCGA-33-4583 TCGA-33-4587 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2608 
       97.94       151.27        54.44         6.94       118.36        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
       65.23        81.24        74.66        60.30        50.66        44.75 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4129 TCGA-37-4130 
        4.96         1.12        26.43        33.90         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5016 TCGA-39-5019 
        7.46         7.82         3.39        37.58       126.58       111.35 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
       55.20        82.52         1.71        24.33         1.94        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       68.38        71.18        17.06        39.12        33.11        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6773 TCGA-43-7656 TCGA-43-A475 TCGA-43-A56U 
       22.98        24.89         3.81        19.59         9.73        14.20 
TCGA-46-3767 TCGA-46-6026 TCGA-51-4079 TCGA-52-7811 TCGA-56-6545 TCGA-56-7582 
       13.02        13.91         0.39         8.75        21.90        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8304 TCGA-56-8307 
        6.51         0.10        17.49        33.24         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       20.94        18.74        14.47         0.03        13.25        13.55 
TCGA-58-8391 TCGA-58-A46J TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2704 
       71.24        85.12        29.92        21.11        12.23        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 
       92.71        21.93        80.45        49.48        66.54        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 
       48.49        42.64         3.19        29.85        23.57        26.83 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       52.67        70.13        70.42        68.15        55.30       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MY TCGA-66-2742 
       70.62        58.65        45.57        89.29        34.59        21.07 
TCGA-66-2744 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
        0.99         0.99        21.01         0.99         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        7.07        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
       25.97        22.98         4.04        10.06        54.08        49.05 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 
        6.64         6.94        13.35        73.12       140.09         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8133 
       73.22        70.13        46.78         6.51        12.59        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8150 TCGA-77-8153 
       39.09        17.72        11.54        26.40        54.41        65.49 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6560 
       36.36       126.18       132.36         5.92        38.86        41.39 
TCGA-85-7699 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 
       32.91        19.04        24.13        26.79        30.64         0.76 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
       13.22        16.77         2.01        15.39         7.76        36.59 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A510 
       12.59        18.08        22.59        30.28        24.36        15.85 
TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
       15.29        29.92        24.92        11.77        22.62        10.59 
TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-96-8169 
        2.70         5.26         2.30         4.01         5.03        18.31 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       27.68        21.44        21.34        18.15         2.01        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HF 
       20.32        18.58        12.89        16.11        13.41         4.54 
TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NK-A5CR TCGA-NK-A5CX 
        1.22         4.21        49.28        43.92        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         3.72        11.18         0.20 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.13              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           173.82            151.27 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            21.09             21.96 
[1] "0.1 - 173.8 (21.1)" "0.0 - 151.3 (22.0)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         0       45       69        1        32        50
  8P LOSS WILD-TYPE       2       44       83        1        33        45
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  8P LOSS MUTATED           1         35          6        2
  8P LOSS WILD-TYPE         2         28         13        5
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                45                44
  STAGE IB                69                83
  STAGE II                 1                 1
  STAGE IIA               32                33
  STAGE IIB               50                45
  STAGE III                1                 2
  STAGE IIIA              35                28
  STAGE IIIB               6                13
  STAGE IV                 2                 5
[1] 10  2
[1] 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    53 144  38   8
  8P LOSS WILD-TYPE  59 150  33  16
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              53                59
  T2             144               150
  T3              38                33
  T4               8                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 LOSS MUTATED   149  69  22   2
  8P LOSS WILD-TYPE 168  64  18   3
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0             149               168
  N1              69                64
  N2              22                18
  N3               2                 3
[1] 4 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   201   2
  8P LOSS WILD-TYPE 210   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    201    2
  8P LOSS WILD-TYPE  210    5
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             201               210
  1               2                 5
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    58 185
  8P LOSS WILD-TYPE  72 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     58  185
  8P LOSS WILD-TYPE   72  186
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              58                72
  MALE               185               186
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   176  33
  8P LOSS WILD-TYPE 208  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    176   33
  8P LOSS WILD-TYPE  208   20
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              176               208
  YES              33                20
[1] 2 2
[1] FALSE
D56V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                       6
  8P LOSS WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  8P LOSS MUTATED                                        1
  8P LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                         0
  8P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                           236
  8P LOSS WILD-TYPE                                                         243
D56V10, multiclass
                                                             clus
vv                                                            8P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             236
                                                             clus
vv                                                            8P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               243
[1] 4 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   197   5   2  13
  8P LOSS WILD-TYPE 202   7   2  10
D56V13, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             197               202
  R1               5                 7
  R2               2                 2
  RX              13                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                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       4                        13   170
  8P LOSS WILD-TYPE     5                        18   179
D56V14, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              13                18
  WHITE                                 170               179
[1] 3 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     3 150
  8P LOSS WILD-TYPE   5 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3  150
  8P LOSS WILD-TYPE    5  167
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO             150               167
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    31  20
  8Q LOSS WILD-TYPE 249 194
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               51               443 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               194 
$`8Q LOSS MUTATED`
TCGA-18-5595 TCGA-90-7766 TCGA-NC-A5HE TCGA-NC-A5HM TCGA-21-1072 TCGA-22-5483 
       27.19         9.50        76.80        39.85        99.16        18.84 
TCGA-33-4566 TCGA-33-4586 TCGA-33-6738 TCGA-37-3792 TCGA-37-4135 TCGA-37-4141 
      173.82        14.07        63.35         0.39         6.81         0.39 
TCGA-39-5011 TCGA-39-5037 TCGA-43-6771 TCGA-46-6025 TCGA-52-7622 TCGA-52-7809 
      133.25        55.56         5.46        10.65        28.34         5.46 
TCGA-56-7730 TCGA-56-8629 TCGA-56-A4BW TCGA-58-8390 TCGA-58-A46K TCGA-63-A5MP 
        6.51        15.81        19.23        29.95        34.36        25.28 
TCGA-63-A5MS TCGA-66-2727 TCGA-66-2766 TCGA-66-2791 TCGA-70-6723 TCGA-77-8144 
       78.28        16.96         1.02         5.03        12.33        27.39 
TCGA-77-8154 TCGA-77-A5GF TCGA-85-6561 TCGA-85-7844 TCGA-85-8070 TCGA-85-8276 
       60.53        27.62        40.24        29.95        31.56        34.52 
TCGA-85-8277 TCGA-85-8352 TCGA-85-A4CN TCGA-85-A50M TCGA-85-A53L TCGA-90-A4ED 
       10.09         5.29        34.13        27.16        12.39        20.22 
TCGA-94-8491 TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL 
       26.63        20.71        11.84        57.30        13.74         2.89 
TCGA-NC-A5HP TCGA-O2-A52S TCGA-O2-A52V 
       25.32        12.72        43.89 

$`8Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
      129.01       133.74         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       31.27        17.88        22.49        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
        2.93        11.61        12.03        19.99        13.05         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       17.00        16.77        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 
       41.42         9.01        35.34        32.32        66.61         8.02 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       20.78        42.08        30.81        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
       18.38        16.14        57.07        19.36         2.76         5.69 
TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
       21.21        19.10         0.07        40.90        65.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        0.43         8.58        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       92.15        36.07        92.42        86.96         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
       49.94       119.54        46.88        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       15.58        31.73       122.43         9.34       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
       31.63        88.11        41.69        33.93        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        7.33         4.31        64.21         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       20.48        35.08        48.33        24.13         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       34.75        13.12        32.02        19.30         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       63.55        14.63        44.25         0.79        86.30        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       79.20        11.74        30.12        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-A4WN 
       97.94        79.53       103.53       151.27        54.44         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        0.30        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       39.32         4.96         1.12        38.79         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       33.90         4.01         0.43         7.96         8.12         7.46 
TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 
        7.82         3.39        37.58        21.70       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 
        1.94        60.53        36.39        68.38        71.18        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       40.21        38.66        39.12        33.11        27.91        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       24.89        21.47         3.81        19.59        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
        9.73        14.20        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 
        4.44        13.91         0.39         0.39        29.95        30.35 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        8.75        27.45        28.96        12.43        18.25        21.90 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 
       18.48        14.53        31.27        30.41        19.76         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       17.49        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
        9.93        20.25        20.94        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 
       14.47         0.03        13.25        13.55        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       34.78        85.12        56.65        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       12.23        10.22        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       80.45        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       11.34        89.29        16.37        36.16        53.88        34.59 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       43.10         2.01        21.07         0.99         1.02         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        0.92         0.99        43.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
        2.01         2.01         2.01         7.07        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        3.02         2.01        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       24.95         1.97        25.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
       22.98        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         6.94        13.35        16.18        14.73 
TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.07        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
       46.78        32.55         6.51        86.76        55.73        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
      156.66        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       11.54        26.40         6.97        66.51        54.41        65.49 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       36.36       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
       61.94        38.86         9.67        41.39         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 
       34.95        31.30        32.91         1.38         1.15        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 
       25.15        19.04        24.13        26.79        30.64         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       13.22        22.45        16.77         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
       15.39         7.76        36.59        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       22.59        30.28        30.97        19.86        24.36        30.48 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       19.73        16.21        15.85        14.96        15.29        29.92 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
        3.65        24.92         2.93        11.77        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
        2.70         3.48         4.01         5.26         2.30         4.01 
TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        5.03        14.14        17.69        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       27.68        21.44        30.81        30.67        21.34        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
       18.15         2.01        27.02        20.32        18.58        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       16.11        13.18        13.41         4.54        64.54         1.22 
TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
        4.21        49.28        43.92        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A5IB TCGA-XC-AA0X 
        3.65        33.07         3.72        11.18         0.20 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.39              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           173.82            156.66 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            25.28             21.70 
[1] "0.4 - 173.8 (25.3)" "0.0 - 156.7 (21.7)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         0        5       18        1        13         8
  8Q LOSS WILD-TYPE       2       84      134        1        52        87
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  8Q LOSS MUTATED           1          6          1        1
  8Q LOSS WILD-TYPE         2         57         18        6
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 5                84
  STAGE IB                18               134
  STAGE II                 1                 1
  STAGE IIA               13                52
  STAGE IIB                8                87
  STAGE III                1                 2
  STAGE IIIA               6                57
  STAGE IIIB               1                18
  STAGE IV                 1                 6
[1] 10  2
[1] 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     9  39   5   1
  8Q LOSS WILD-TYPE 103 255  66  23
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               9               103
  T2              39               255
  T3               5                66
  T4               1                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                 N0  N1  N2  N3
  8Q LOSS MUTATED    32  15   5   1
  8Q LOSS WILD-TYPE 285 118  35   4
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              32               285
  N1              15               118
  N2               5                35
  N3               1                 4
[1] 4 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    45   1
  8Q LOSS WILD-TYPE 366   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     45    1
  8Q LOSS WILD-TYPE  366    6
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              45               366
  1               1                 6
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    10  44
  8Q LOSS WILD-TYPE 120 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10   44
  8Q LOSS WILD-TYPE  120  327
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              10               120
  MALE                44               327
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    34  10
  8Q LOSS WILD-TYPE 350  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     34   10
  8Q LOSS WILD-TYPE  350   43
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               34               350
  YES              10                43
[1] 2 2
[1] FALSE
D57V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED                                       2
  8Q LOSS WILD-TYPE                                    13
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  8Q LOSS MUTATED                                        1
  8Q LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED                                         0
  8Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                            51
  8Q LOSS WILD-TYPE                                                         428
D57V10, multiclass
                                                             clus
vv                                                            8Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              51
                                                             clus
vv                                                            8Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               428
[1] 4 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    42   2   0   3
  8Q LOSS WILD-TYPE 357  10   4  20
D57V13, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              42               357
  R1               2                10
  R2               0                 4
  RX               3                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       3                         1    38
  8Q LOSS WILD-TYPE     6                        30   311
D57V14, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               1                30
  WHITE                                  38               311
[1] 3 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  30
  8Q LOSS WILD-TYPE   7 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   30
  8Q LOSS WILD-TYPE    7  287
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              30               287
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   179 132
  9P LOSS WILD-TYPE 101  82
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              311               183 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              132                82 
$`9P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-4083 TCGA-21-A5DI TCGA-22-5471 TCGA-22-5472 
       12.20       123.19         6.18        32.19        60.66        64.93 
TCGA-22-A5C4 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-43-5668 
       22.06        19.76        31.50        28.96        31.27        18.38 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 
        7.76         2.93        11.61        12.03        19.99        13.05 
TCGA-56-8305 TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 TCGA-60-2721 TCGA-63-A5MH 
        3.45        21.04         3.58        41.42        32.32        66.61 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7545 
        9.50        14.07        21.04         0.16        18.38        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD TCGA-NK-A5CT TCGA-NK-A5D1 
       19.36         2.76         5.69         0.07        65.65        16.80 
TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
        8.58       117.57        11.34        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
       92.42         2.79        49.94       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 
       70.16        34.78       122.43       119.80        43.23        88.11 
TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       33.93        10.82         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4601 
       27.02        20.48        35.08        48.33        38.17        34.75 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       19.30         9.57        11.77        14.63        44.25         0.79 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 
       11.74        18.84        30.12        56.32        97.94        79.53 
TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB 
      103.53        54.44        63.35         4.70        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
      110.99        44.19        27.16         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       65.23        81.24        16.93        44.75         4.96        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3789 TCGA-37-4130 TCGA-37-4135 
        4.04        26.43        33.90         0.43         8.12         6.81 
TCGA-37-4141 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 
        0.39        37.58       133.25       126.58       111.35       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 
        1.71        24.33        60.53        36.39        68.38        17.06 
TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
       40.21        39.12        33.11        27.91        24.89        21.47 
TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-46-3765 TCGA-46-3766 
        5.46        19.59        13.38        11.77        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 
       13.02         9.83         4.44        13.91        29.95         5.46 
TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
       30.35        28.96        12.43        18.25        21.90        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       14.53        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       17.49        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       14.07         1.35         1.81        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS 
       20.25        15.81        20.94        19.23        13.32         0.26 
TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       13.25        29.95        71.24        16.47        34.78        85.12 
TCGA-58-A46L TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       56.65        10.22        96.82        92.71        21.93        80.45 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       42.64         3.19        35.90        23.57        26.83        11.77 
TCGA-63-7020 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MR 
       70.13        68.15        55.30        70.62        58.65        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
       78.28        16.37        53.88        16.96        43.10         2.01 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2759 TCGA-66-2763 
       21.07         1.02         0.92         0.99        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
        2.01         1.02         2.01         7.07        19.00         3.02 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 
       19.00        12.03         3.98        12.00         1.97        25.97 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-66-2794 TCGA-68-7757 
       22.98         4.04        22.98        10.06        54.08         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-70-6723 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       13.35        16.18        12.33        73.12        75.09        23.28 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        0.49        73.22        70.13       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8138 
       32.55        86.76        55.73        37.81       156.66        17.72 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
       11.54        26.40        27.39         6.97        66.51        65.49 
TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH 
       60.53       132.36        22.29         5.92        61.94        38.86 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       41.39        36.53        34.95        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       29.95        18.94        25.15         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
       16.77         5.29        15.39        36.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50M 
       30.28        34.13        30.97        19.86        19.73        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96        29.92        12.39         3.65 
TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
        2.93        22.62        10.59         2.70         3.48         4.01 
TCGA-92-8065 TCGA-94-8035 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 
        2.30         4.01        14.14        17.69        18.31        17.46 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A 
       27.68        30.81        30.67        21.34        27.16        18.15 
TCGA-98-A53B TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 
        2.01        20.71        12.89        16.11        13.41        11.84 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
       64.54        57.30        43.92        25.32        14.73        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       83.57         3.65         3.72        12.72        43.89 

$`9P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 
        4.47         4.80        31.99        27.19        14.93        48.82 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-39-5039 TCGA-43-2578 TCGA-43-7658 
      129.01       133.74         1.55        17.88        22.49        78.18 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2712 TCGA-60-2715 
       17.00        16.77        17.85         0.13         9.01        35.34 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-94-A5I4 TCGA-98-A53D 
        8.02        20.78        42.08        30.81        16.14        21.21 
TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3408 
       19.10        76.80        39.85        40.90         0.43        75.75 
TCGA-18-3421 TCGA-18-4721 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
       86.96       154.32        60.89        15.58        31.73         9.34 
TCGA-21-5782 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-4595 TCGA-22-4596 
       31.63        41.69        21.99         7.33        24.13         0.56 
TCGA-22-4604 TCGA-22-4605 TCGA-22-5473 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       13.12        32.02        63.55        86.30        71.34        79.20 
TCGA-22-5489 TCGA-22-5492 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-A5GW 
       62.86        16.64       173.82       151.27        14.07         0.30 
TCGA-33-AASJ TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 
      118.36        74.66         9.07        60.30        50.66        39.32 
TCGA-34-7107 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
        1.12         4.01         0.39         7.96         7.46         7.82 
TCGA-37-5819 TCGA-37-A5EN TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5030 
        3.39        21.70        68.58        55.20        82.52         1.94 
TCGA-39-5036 TCGA-39-5037 TCGA-43-2581 TCGA-43-6143 TCGA-43-6773 TCGA-43-A475 
       71.18        55.56        38.66        22.98         3.81         9.73 
TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 
       14.20        10.65         0.39         0.39        28.34         8.75 
TCGA-52-7812 TCGA-56-8623 TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 
       27.45        22.75        18.74        14.47         0.03        13.55 
TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2704 
       34.36        35.24        29.92        21.11        12.23        37.94 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2722 
       49.48        66.54        56.91        50.33        48.49        29.85 
TCGA-63-6202 TCGA-63-7021 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
       52.67        70.42       102.67        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2744 TCGA-66-2754 
       11.34        25.28        36.16        34.59         0.99         2.01 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2767 TCGA-66-2770 TCGA-66-2777 TCGA-66-2783 
       43.99        21.01         2.01        23.01         2.01        24.95 
TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
       40.01         5.03        30.02         4.01        49.05         2.73 
TCGA-68-7756 TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-7138 TCGA-77-7139 
        6.64        14.73        12.07        29.56        11.18       140.09 
TCGA-77-8007 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8150 
        6.51        12.59        53.92        39.09       104.09        54.41 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 
       36.36       126.18       150.25        27.62         9.67        40.24 
TCGA-85-6798 TCGA-85-7698 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
        6.41        31.30        19.04        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       30.64        34.52        10.09         3.09        32.71         2.01 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A512 
        7.76        38.14        12.59        24.36        30.48        15.29 
TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-92-8064 TCGA-94-8490 TCGA-94-8491 
       24.92        11.77        20.22         5.26         5.03        26.63 
TCGA-96-7544 TCGA-98-7454 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-LA-A446 
       71.01        21.44        27.02        20.32        18.58        13.18 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
        4.54         1.22        13.74         4.21         2.89        49.28 
TCGA-O2-A52N TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07        11.18         0.20 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           156.66            173.82 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            21.04             23.01 
[1] "0.1 - 156.7 (21.0)" "0.0 - 173.8 (23.0)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         1       62       98        1        41        51
  9P LOSS WILD-TYPE       1       27       54        1        24        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  9P LOSS MUTATED           2         44          9        5
  9P LOSS WILD-TYPE         1         19         10        2
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                62                27
  STAGE IB                98                54
  STAGE II                 1                 1
  STAGE IIA               41                24
  STAGE IIB               51                44
  STAGE III                2                 1
  STAGE IIIA              44                19
  STAGE IIIB               9                10
  STAGE IV                 5                 2
[1] 10  2
[1] 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    75 181  45  14
  9P LOSS WILD-TYPE  37 113  26  10
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              75                37
  T2             181               113
  T3              45                26
  T4              14                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
  9P LOSS MUTATED   208  76  27   2
  9P LOSS WILD-TYPE 109  57  13   3
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             208               109
  N1              76                57
  N2              27                13
  N3               2                 3
[1] 4 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   256   5
  9P LOSS WILD-TYPE 155   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    256    5
  9P LOSS WILD-TYPE  155    2
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             256               155
  1               5                 2
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    84 231
  9P LOSS WILD-TYPE  46 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     84  231
  9P LOSS WILD-TYPE   46  140
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              84                46
  MALE               231               140
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   238  33
  9P LOSS WILD-TYPE 146  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    238   33
  9P LOSS WILD-TYPE  146   20
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              238               146
  YES              33                20
[1] 2 2
[1] FALSE
D58V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                       6
  9P LOSS WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  9P LOSS MUTATED                                        2
  9P LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                         1
  9P LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                           306
  9P LOSS WILD-TYPE                                                         173
D58V10, multiclass
                                                             clus
vv                                                            9P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             306
                                                             clus
vv                                                            9P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
D58V12, continuous
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED   249   6   3  14
  9P LOSS WILD-TYPE 150   6   1   9
D58V13, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             249               150
  R1               6                 6
  R2               3                 1
  RX              14                 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                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       6                        21   221
  9P LOSS WILD-TYPE     3                        10   128
D58V14, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   6                 3
  BLACK OR AFRICAN AMERICAN              21                10
  WHITE                                 221               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     4 204
  9P LOSS WILD-TYPE   4 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  204
  9P LOSS WILD-TYPE    4  113
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO             204               113
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   145  98
  9Q LOSS WILD-TYPE 135 116
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              243               251 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               98               116 
$`9Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1017 TCGA-22-A5C4 
       12.20       123.19         6.18        32.19        48.82        22.06 
TCGA-33-4532 TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 TCGA-43-7657 TCGA-43-8118 
      129.01        19.76        31.50        31.27         7.76         2.93 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-A4ZJ TCGA-60-2696 
       12.03        19.99        13.05         3.45        21.04         3.58 
TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-90-7766 TCGA-90-7964 
        9.01        32.32        66.61         8.02         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD 
       21.04         0.16        18.38         2.76         5.69         0.07 
TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3414 TCGA-18-3417 
       39.85        65.65        16.80         8.58        23.54        36.07 
TCGA-18-3419 TCGA-21-1070 TCGA-21-1075 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       92.42       119.54        70.16       119.80        43.23        31.63 
TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       33.93        10.82         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4607 TCGA-22-5474 
       27.02        20.48        35.08        48.33        19.30        14.63 
TCGA-22-5478 TCGA-22-5482 TCGA-33-4547 TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 
        0.79        11.74        79.53       103.53        54.44        63.35 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2608 TCGA-34-5231 
        6.94       110.99        44.19        27.16        32.88        65.23 
TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 
       81.24        16.93        44.75        39.32         4.96        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 
        4.04        26.43        33.90         8.12         6.81         0.39 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5024 TCGA-39-5028 TCGA-39-5031 
      133.25       126.58       111.35        82.52         1.71        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-43-2576 TCGA-43-3920 TCGA-43-5670 
       36.39        68.38        55.56        40.21        33.11        27.91 
TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-46-3766 
       24.89         5.46        19.59        13.38        11.77        12.16 
TCGA-46-3767 TCGA-46-6026 TCGA-51-4081 TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 
       13.02        13.91        29.95        30.35        28.96        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       18.25        21.90        18.48        14.53        31.27        30.41 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 TCGA-56-8503 
        0.10        17.49        14.96         3.48        26.89         1.35 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.81        13.81         9.93        20.25        15.81        20.94 
TCGA-56-A5DS TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-60-2698 
        0.26        29.95        16.47        34.78        85.12        10.22 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
       96.82        92.71        80.45        50.33        42.64         3.19 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 
       35.90        23.57        26.83        11.77        70.13        68.15 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       70.62        58.65        78.28        16.37        36.16        53.88 
TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 
       34.59        43.10         2.01        21.07         1.02         0.92 
TCGA-66-2756 TCGA-66-2759 TCGA-66-2763 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
        0.99        25.05         0.99         7.07        19.00         3.02 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 
       19.00        12.03         3.98        12.00         1.97        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
        4.04        22.98        10.06         6.94        13.35        16.18 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7337 
       12.33        29.56        73.12        75.09        23.28       106.95 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8138 
       46.78         6.51        86.76        37.81       156.66        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 
      104.09        11.54        26.40         6.97        66.51        60.53 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 
      132.36        22.29         5.92        61.94        38.86        41.39 
TCGA-85-7697 TCGA-85-7843 TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       34.95         1.15        25.15         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC 
       16.77         5.29        18.08        22.59        30.97        19.86 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       19.73        27.16        16.21        15.85        14.96        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       12.39         3.65         2.93        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8065 TCGA-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        3.48         2.30         4.01        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       71.01        18.31        17.46        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53B TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG 
       27.16         2.01        12.89        13.41         4.54        64.54 
TCGA-NC-A5HI TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX 
       57.30        49.28        25.32        14.73        26.43         3.65 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB 
        3.72        43.89        11.18 

$`9Q LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 TCGA-22-5471 
        4.47         4.80        31.99        27.19        14.93        60.66 
TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 
       64.93       133.74         1.55        28.96        17.88        22.49 
TCGA-43-5668 TCGA-43-7658 TCGA-43-A474 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY 
       18.38        78.18        11.61        17.00        16.77        17.85 
TCGA-56-A5DR TCGA-60-2711 TCGA-60-2715 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
        0.13        41.42        35.34        20.78        42.08        30.81 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE 
       16.14        57.07        19.36        21.21        19.10        76.80 
TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
       40.90         0.43        75.75       117.57        11.34        92.15 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 
       86.96         2.79       154.32        49.94        46.88        99.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       60.89        34.78        15.58        31.73       122.43         9.34 
TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-4595 TCGA-22-4596 
       88.11        41.69        21.99         7.33        24.13         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 
       38.17        34.75        13.12        32.02         9.57        11.77 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 
       63.55        44.25        86.30        71.34        79.20        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4566 
       30.12        62.86        56.32        16.64        97.94       173.82 
TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ 
      151.27        14.07         4.70         0.30        36.62       118.36 
TCGA-34-2596 TCGA-34-2600 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
        2.63        61.61        74.66         9.07        60.30        50.66 
TCGA-34-7107 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
        1.12         4.01         0.43         0.39         7.96         7.46 
TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5021 TCGA-39-5022 
        7.82         3.39        37.58        21.70        68.58        55.20 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5036 TCGA-39-5040 TCGA-43-2581 
      102.18        24.33         1.94        71.18        17.06        38.66 
TCGA-43-3394 TCGA-43-6143 TCGA-43-6770 TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U 
       39.12        22.98        21.47         3.81         9.73        14.20 
TCGA-46-3765 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
       13.32         9.83         4.44        10.65         0.39         0.39 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-7582 TCGA-56-7730 
       28.34         5.46         8.75        27.45        19.76         6.51 
TCGA-56-7823 TCGA-56-8083 TCGA-56-8309 TCGA-56-8623 TCGA-56-8625 TCGA-56-A4BW 
       33.24         4.93        14.07        22.75        10.36        19.23 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       13.32        18.74        14.47         0.03        13.25        13.55 
TCGA-58-8391 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       71.24        34.36        56.65        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       12.23        37.94        21.93        49.48        66.54        56.91 
TCGA-60-2716 TCGA-60-2722 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MB 
       48.49        29.85        52.67        70.42        55.30       102.67 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       59.97        45.57        14.99        11.34        25.28        89.29 
TCGA-66-2727 TCGA-66-2744 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2765 
       16.96         0.99         2.01        43.99        21.01         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2777 TCGA-66-2783 
        1.02         2.01         2.01        23.01         2.01        24.95 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
       25.97        40.01         5.03        30.02        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59J TCGA-70-6722 TCGA-77-7138 
       49.05         2.73         6.64        14.73        12.07        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7465 
      140.09         0.49        73.22        70.13         0.16        32.55 
TCGA-77-8009 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8144 TCGA-77-8150 
       55.73        12.59        53.92        39.09        27.39        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6175 
       65.49        36.36       126.18       150.25        27.62         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
       40.24         6.41        36.53        31.30        32.91         1.38 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       29.95        18.94        19.04        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       30.64        34.52        10.09         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL 
       15.39         7.76        36.59        38.14        12.59        30.28 
TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A512 TCGA-90-6837 TCGA-90-7769 
       34.13        24.36        30.48        15.29        24.92        11.77 
TCGA-90-A4ED TCGA-92-8063 TCGA-92-8064 TCGA-94-8490 TCGA-96-A4JL TCGA-98-7454 
       20.22         4.01         5.26         5.03        27.68        21.44 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 
       18.15        27.02        20.32        18.58        20.71        16.11 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       13.18        11.84         1.22        13.74         4.21         2.89 
TCGA-NC-A5HO TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52S TCGA-XC-AA0X 
       43.92        83.57        33.07        12.72         0.20 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           156.66            173.82 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            21.04             22.75 
[1] "0.1 - 156.7 (21.0)" "0.0 - 173.8 (22.8)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         1       50       66        1        33        51
  9Q LOSS WILD-TYPE       1       39       86        1        32        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  9Q LOSS MUTATED           2         31          7        5
  9Q LOSS WILD-TYPE         1         32         12        2
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                50                39
  STAGE IB                66                86
  STAGE II                 1                 1
  STAGE IIA               33                32
  STAGE IIB               51                44
  STAGE III                2                 1
  STAGE IIIA              31                32
  STAGE IIIB               7                12
  STAGE IV                 5                 2
[1] 10  2
[1] 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    59 140  40   8
  9Q LOSS WILD-TYPE  53 154  31  16
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              59                53
  T2             140               154
  T3              40                31
  T4               8                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
  9Q LOSS MUTATED   157  69  17   2
  9Q LOSS WILD-TYPE 160  64  23   3
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             157               160
  N1              69                64
  N2              17                23
  N3               2                 3
[1] 4 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   197   5
  9Q LOSS WILD-TYPE 214   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    197    5
  9Q LOSS WILD-TYPE  214    2
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             197               214
  1               5                 2
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    65 182
  9Q LOSS WILD-TYPE  65 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     65  182
  9Q LOSS WILD-TYPE   65  189
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              65                65
  MALE               182               189
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   196  19
  9Q LOSS WILD-TYPE 188  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    196   19
  9Q LOSS WILD-TYPE  188   34
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              196               188
  YES              19                34
[1] 2 2
[1] FALSE
D59V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                       4
  9Q LOSS WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  9Q LOSS MUTATED                                        1
  9Q LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                         1
  9Q LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                           241
  9Q LOSS WILD-TYPE                                                         238
D59V10, multiclass
                                                             clus
vv                                                            9Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             241
                                                             clus
vv                                                            9Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               238
[1] 4 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   194   3   2   9
  9Q LOSS WILD-TYPE 205   9   2  14
D59V13, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0             194               205
  R1               3                 9
  R2               2                 2
  RX               9                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       5                        18   170
  9Q LOSS WILD-TYPE     4                        13   179
D59V14, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   5                 4
  BLACK OR AFRICAN AMERICAN              18                13
  WHITE                                 170               179
[1] 3 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     1 161
  9Q LOSS WILD-TYPE   7 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1  161
  9Q LOSS WILD-TYPE    7  156
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO             161               156
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED   124  88
  10P LOSS WILD-TYPE 156 126
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               212                282 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                88                126 
$`10P LOSS MUTATED`
TCGA-18-3406 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-33-4533 
       12.20         6.18        27.19        32.19        14.93       133.74 
TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-8118 TCGA-43-A56V TCGA-56-8305 
       28.96        17.88        22.49         2.93        12.03         3.45 
TCGA-56-A4BY TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GB TCGA-94-7033 
       17.85        35.34        66.61         8.02        30.81        21.04 
TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH 
        0.16        16.14        19.36         2.76         5.69        19.10 
TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3411 
        0.07        39.85        40.90        65.65        16.80       117.57 
TCGA-18-3412 TCGA-18-3421 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
       11.34        86.96        49.94        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5786 
       60.89        34.78        31.73       122.43       119.80        33.93 
TCGA-22-0940 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       21.99        64.21         1.74        27.02        20.48        35.08 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5477 
       24.13        38.17         9.57        11.77        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4538 
        0.79        86.30        11.74        18.84        56.32        97.94 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD 
      103.53       151.27        14.07         0.30        36.62       110.99 
TCGA-34-2596 TCGA-34-5236 TCGA-34-5927 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3789 
        2.63         9.07        44.75        26.43        33.90         0.43 
TCGA-37-3792 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5019 TCGA-39-5021 
        0.39         6.81         3.39        21.70       111.35        68.58 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
      102.18        24.33         1.94        60.53        36.39        71.18 
TCGA-43-2576 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-43-A56U TCGA-46-3765 
       40.21        33.11        22.98        21.47        14.20        13.32 
TCGA-46-3769 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
        4.44         0.39        29.95        28.34         5.46        30.35 
TCGA-56-1622 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
       28.96        18.25        14.53        30.41        19.76         6.51 
TCGA-56-7823 TCGA-56-8307 TCGA-56-8503 TCGA-56-8622 TCGA-56-8626 TCGA-56-8628 
       33.24        26.89         1.35         1.81         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8391 
       15.81        20.94        18.74        14.47         0.03        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 
       16.47        34.78        85.12        34.36        35.24        21.11 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2719 
       96.82        37.94        80.45        49.48        66.54        42.64 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 TCGA-63-A5MB 
       29.85        35.90        26.83        70.13        70.42       102.67 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MP TCGA-66-2727 
       58.65        59.97        45.57        14.99        25.28        16.96 
TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
        2.01         1.02         2.01         0.92        43.99        21.01 
TCGA-66-2759 TCGA-66-2770 TCGA-66-2777 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
       25.05        23.01         2.01        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        4.04         5.03        10.06        49.05         2.73         6.64 
TCGA-68-8251 TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 
       13.35        14.73        12.33        29.56        23.28        11.18 
TCGA-77-7139 TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
      140.09        32.55        55.73       156.66        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 TCGA-77-8156 
       17.72       104.09        11.54        27.39        65.49        36.36 
TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 
       27.62         6.41        36.53        32.91        29.95        18.94 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8351 TCGA-85-8353 
       24.13        31.56        26.79        10.09        16.77         3.09 
TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ 
       32.71        15.39        36.59        34.13        19.86        30.48 
TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-A4EE TCGA-92-8064 TCGA-94-8035 TCGA-94-A5I6 
       19.73         3.65        22.62         5.26         4.01        17.69 
TCGA-96-8170 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53J 
       17.46        30.81        21.34        27.16        18.15        20.71 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HO TCGA-O2-A52S 
       16.11        13.18        13.41        11.84        43.92        12.72 
TCGA-O2-A52V TCGA-O2-A5IB 
       43.89        11.18 

$`10P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-1017 TCGA-22-5471 
        4.47       123.19         4.80        31.99        48.82        60.66 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       64.93        22.06       129.01         1.55        19.76        31.50 
TCGA-34-2609 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-56-7221 
       31.27        18.38         7.76        78.18        11.61        19.99 
TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       13.05        17.00        16.77        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 
       41.42         9.01        32.32        20.78        42.08         9.50 
TCGA-90-7964 TCGA-94-7943 TCGA-96-7545 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A7XE 
       14.07        18.38        57.07        21.21        76.80         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
        8.58        75.75        23.54        92.15        36.07        92.42 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1078 TCGA-21-1081 TCGA-21-1083 
        2.79       154.32       119.54        15.58         9.34        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 
       31.63        88.11        41.69        10.82         7.33         4.31 
TCGA-22-1012 TCGA-22-4594 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       14.10        48.33         0.56        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 
       19.30        63.55        71.34        79.20        30.12        62.86 
TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
       16.64        79.53       173.82        54.44        63.35         4.70 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 
        6.94        44.19       118.36        27.16        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       65.23        81.24        74.66        60.30        50.66        16.93 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 
       39.32         4.96         1.12        38.79         4.04         4.01 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-A5EL 
        7.96         8.12         7.46         7.82         0.39        37.58 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5035 
      133.25       126.58        55.20        82.52         1.71        68.38 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6647 
       55.56        17.06        38.66        39.12        27.91        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
        5.46         3.81        19.59        13.38        11.77         9.73 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       12.16        13.02         9.83        10.65        13.91         0.39 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 
        8.75        27.45        12.43        21.90        18.48        31.27 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 
        0.10        17.49        14.96         4.93         3.48        14.07 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS 
       22.75        13.81        10.36        19.23        13.32         0.26 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46L TCGA-58-A46N TCGA-60-2697 
       13.25        13.55        29.95        56.65        29.92        12.23 
TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       10.22        92.71        21.93        56.91        50.33        48.49 
TCGA-60-2720 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7022 TCGA-63-7023 
        3.19        23.57        11.77        52.67        68.15        55.30 
TCGA-63-A5MG TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       70.62        11.34        89.29        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 
       53.88        34.59        43.10        21.07         0.99         0.99 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
        0.99         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
       19.00         3.02        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
       24.95         1.97        22.98        30.02        54.08         4.01 
TCGA-68-7757 TCGA-68-A59I TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 TCGA-77-7141 
        6.94        16.18        12.07        73.12        75.09         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
       73.22        70.13       106.95         0.16        46.78         6.51 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
       86.76        37.81        12.59        26.40         6.97        66.51 
TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
       54.41        60.53       126.18       132.36       150.25        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
        5.92        61.94        38.86         9.67        41.39        40.24 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 
       34.95        31.30         1.38         1.15        25.15        19.04 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 
       30.64        34.52         0.76        13.22        22.45         5.29 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        2.01         7.76        38.14        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       30.28        30.97        24.36        27.16        16.21        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 
       14.96        15.29        29.92        12.39        24.92         2.93 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       11.77        20.22        10.59         2.70         3.48         4.01 
TCGA-92-8065 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        2.30         5.03        26.63        14.14        71.01        18.31 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       27.68        21.44        30.67         2.01        27.02        20.32 
TCGA-98-A53I TCGA-L3-A4E7 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       18.58        12.89         4.54        64.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ 
       13.74         4.21         2.89        49.28        25.32        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-XC-AA0X 
       26.43        83.57         3.65        33.07         3.72         0.20 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.03               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            156.66             173.82 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            23.705             20.105 
[1] "0.0 - 156.7 (23.7)" "0.1 - 173.8 (20.1)"
[1] "hr=" "1.1"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         0       35       75        1        26        39
  10P LOSS WILD-TYPE       2       54       77        1        39        56
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  10P LOSS MUTATED           2         27          7        1
  10P LOSS WILD-TYPE         1         36         12        6
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 35                 54
  STAGE IB                 75                 77
  STAGE II                  1                  1
  STAGE IIA                26                 39
  STAGE IIB                39                 56
  STAGE III                 2                  1
  STAGE IIIA               27                 36
  STAGE IIIB                7                 12
  STAGE IV                  1                  6
[1] 10  2
[1] 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    47 129  30   9
  10P LOSS WILD-TYPE  65 165  41  15
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               47                 65
  T2              129                165
  T3               30                 41
  T4                9                 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
  10P LOSS MUTATED   139  53  19   2
  10P LOSS WILD-TYPE 178  80  21   3
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0              139                178
  N1               53                 80
  N2               19                 21
  N3                2                  3
[1] 4 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   182   1
  10P LOSS WILD-TYPE 229   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    182    1
  10P LOSS WILD-TYPE  229    6
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0              182                229
  1                1                  6
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    52 163
  10P LOSS WILD-TYPE  78 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     52  163
  10P LOSS WILD-TYPE   78  208
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               52                 78
  MALE                163                208
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   166  24
  10P LOSS WILD-TYPE 218  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    166   24
  10P LOSS WILD-TYPE  218   29
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO               166                218
  YES               24                 29
[1] 2 2
[1] FALSE
D60V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                       7
  10P LOSS WILD-TYPE                                     8
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  10P LOSS MUTATED                                        2
  10P LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                         0
  10P LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                           206
  10P LOSS WILD-TYPE                                                         273
D60V10, multiclass
                                                             clus
vv                                                            10P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              206
                                                             clus
vv                                                            10P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
D60V12, continuous
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED   174   5   0  12
  10P LOSS WILD-TYPE 225   7   4  11
D60V13, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0              174                225
  R1                5                  7
  R2                0                  4
  RX               12                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       2                        15   151
  10P LOSS WILD-TYPE     7                        16   198
D60V14, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               15                 16
  WHITE                                  151                198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4 138
  10P LOSS WILD-TYPE   4 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  138
  10P LOSS WILD-TYPE    4  179
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              138                179
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   133  93
  10Q LOSS WILD-TYPE 147 121
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               226                268 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                93                121 
$`10Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1000 TCGA-33-4533 
       12.20         4.47         6.18        32.19        14.93       133.74 
TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V 
       28.96        17.88        22.49        78.18        11.61        12.03 
TCGA-56-7221 TCGA-56-8305 TCGA-56-A4BY TCGA-60-2712 TCGA-60-2715 TCGA-63-A5MH 
       19.99         3.45        17.85         9.01        35.34        66.61 
TCGA-77-A5GB TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       30.81        21.04         0.16        16.14        57.07        19.36 
TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5D1 
        5.69        19.10         0.07        39.85        40.90        16.80 
TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 
        8.58       117.57        11.34       154.32        49.94        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1082 TCGA-21-5783 
       99.16        70.16        60.89        34.78       119.80        88.11 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4595 
       21.99         7.33        64.21         1.74        35.08        24.13 
TCGA-22-4599 TCGA-22-4609 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       38.17         9.57        14.63        44.25         0.79        86.30 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 
       11.74        18.84        56.32        97.94       151.27        14.07 
TCGA-33-6738 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ 
       63.35         0.30        36.62         6.94       110.99       118.36 
TCGA-34-2596 TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-8456 TCGA-34-A5IX 
        2.63         9.07        44.75         4.96        26.43        33.90 
TCGA-37-3792 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 
        0.39         6.81         3.39        21.70       126.58       111.35 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       68.58       102.18        24.33         1.94        60.53        36.39 
TCGA-39-5036 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-6770 TCGA-43-A56U 
       71.18        40.21        39.12        33.11        21.47        14.20 
TCGA-46-3765 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       13.32        10.65         0.39         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 
        5.46        30.35        28.96        18.25        14.53        30.41 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 
       19.76         6.51        33.24        14.96         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
       14.07         1.35         1.81        20.25        15.81        20.94 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8391 
       13.32        18.74        14.47         0.03        13.55        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 
       16.47        34.78        85.12        34.36        35.24        21.11 
TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2719 TCGA-60-2722 
       37.94        80.45        49.48        66.54        42.64        29.85 
TCGA-60-2723 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB 
       35.90        26.83        70.13        70.42        68.15       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-66-2727 TCGA-66-2737 
       70.62        58.65        59.97        45.57        16.96         2.01 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2770 
        1.02         2.01        43.99        21.01        25.05        23.01 
TCGA-66-2773 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
        3.02        12.00         1.97        40.01        22.98         4.04 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        5.03        30.02        10.06        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 TCGA-77-7138 
        6.94        13.35        14.73        12.33        29.56        11.18 
TCGA-77-7139 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8133 TCGA-77-8136 
      140.09        46.78        32.55        55.73        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 
       17.72       104.09        11.54        26.40        27.39        66.51 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6560 TCGA-85-6798 
       65.49        36.36       150.25        27.62        41.39         6.41 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 
       36.53        31.30        32.91        29.95        18.94        24.13 
TCGA-85-8070 TCGA-85-8277 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 
       31.56        10.09        16.77         3.09        32.71        15.39 
TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-90-A4EE 
       36.59        34.13        19.86        30.48        19.73        22.62 
TCGA-92-8064 TCGA-94-8035 TCGA-94-A5I6 TCGA-96-8170 TCGA-98-8021 TCGA-98-8023 
        5.26         4.01        17.69        17.46        30.81        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       27.16        18.15        20.71        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HI TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HT 
       13.41        11.84        57.30        49.28        43.92        26.43 
TCGA-NK-A5CR TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       83.57        43.89        11.18         0.20 

$`10Q LOSS WILD-TYPE`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-22-1017 TCGA-22-5471 
      123.19         4.80        31.99        27.19        48.82        60.66 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       64.93        22.06       129.01         1.55        19.76        31.50 
TCGA-34-2609 TCGA-43-5668 TCGA-43-7657 TCGA-43-8118 TCGA-56-8201 TCGA-56-8308 
       31.27        18.38         7.76         2.93        13.05        17.00 
TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2721 
       16.77        21.04         0.13         3.58        41.42        32.32 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7943 
        8.02        20.78        42.08         9.50        14.07        18.38 
TCGA-98-8020 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A7XE TCGA-18-3408 
        2.76        21.21        76.80        65.65         0.43        75.75 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       23.54        92.15        36.07        92.42        86.96         2.79 
TCGA-21-1070 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
      119.54        15.58        31.73       122.43         9.34        43.23 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-1012 
       31.63        41.69        33.93        10.82         4.31        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 
       27.02        20.48        48.33         0.56        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 
       32.02        19.30        11.77        63.55        71.34        79.20 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       30.12        62.86        16.64        79.53       173.82       103.53 
TCGA-33-4587 TCGA-33-A4WN TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 
       54.44         4.70        44.19        27.16        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       65.23        81.24        74.66        60.30        50.66        16.93 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 
       39.32         1.12        38.79         4.04         4.01         0.43 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-A5EL 
        7.96         8.12         7.46         7.82         0.39        37.58 
TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5035 TCGA-39-5037 
      133.25        55.20        82.52         1.71        68.38        55.56 
TCGA-39-5040 TCGA-43-2581 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 
       17.06        38.66        27.91        22.98        24.89         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-46-3766 
        3.81        19.59        13.38        11.77         9.73        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6026 TCGA-52-7811 TCGA-52-7812 
       13.02         9.83         4.44        13.91         8.75        27.45 
TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 
       12.43        21.90        18.48        31.27         0.10        17.49 
TCGA-56-8083 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-A4BW 
        4.93        22.75        13.81        10.36         9.93        19.23 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8390 TCGA-58-A46L TCGA-58-A46N TCGA-60-2697 
        0.26        13.25        29.95        56.65        29.92        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2713 TCGA-60-2714 
       10.22        96.82        92.71        21.93        56.91        50.33 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 
       48.49         3.19        23.57        11.77        52.67        55.30 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       14.99        11.34        25.28        89.29        78.28        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
       36.16        53.88        34.59        43.10        21.07         0.99 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
        0.92         0.99         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        2.01         7.07        19.00         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 
        3.98        24.95        25.97        22.98        54.08         4.01 
TCGA-68-A59I TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7141 
       16.18        12.07        73.12        75.09        23.28         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 
       73.22        70.13       106.95         0.16         6.51        86.76 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8145 TCGA-77-8150 TCGA-77-8154 
       37.81       156.66        12.59         6.97        54.41        60.53 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH 
      126.18       132.36        22.29         5.92        61.94        38.86 
TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 
        9.67        40.24        34.95         1.38         1.15        25.15 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
       19.04        26.79        30.64        34.52         0.76        13.22 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 
       22.45         5.29         2.01         7.76        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M 
       18.08        22.59        30.28        30.97        24.36        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       16.21        15.85        14.96        15.29        29.92        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A59Q 
        3.65        24.92         2.93        11.77        20.22        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8490 TCGA-94-8491 
        2.70         3.48         4.01         2.30         5.03        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 
       14.14        71.01        18.31        27.68        21.44        30.67 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-NC-A5HF TCGA-NC-A5HG 
        2.01        27.02        20.32        18.58         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HQ 
        1.22        13.74         4.21         2.89        25.32        14.73 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
        3.65        33.07         3.72        12.72 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.03               0.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            154.32             173.82 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             24.13              20.40 
[1] "0.0 - 154.3 (24.1)" "0.1 - 173.8 (20.4)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         1       36       82        1        31        39
  10Q LOSS WILD-TYPE       1       53       70        1        34        56
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  10Q LOSS MUTATED           1         29          7        1
  10Q LOSS WILD-TYPE         2         34         12        6
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 36                 53
  STAGE IB                 82                 70
  STAGE II                  1                  1
  STAGE IIA                31                 34
  STAGE IIB                39                 56
  STAGE III                 1                  2
  STAGE IIIA               29                 34
  STAGE IIIB                7                 12
  STAGE IV                  1                  6
[1] 10  2
[1] 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    49 142  31   7
  10Q LOSS WILD-TYPE  63 152  40  17
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               49                 63
  T2              142                152
  T3               31                 40
  T4                7                 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   149  58  18   2
  10Q LOSS WILD-TYPE 168  75  22   3
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0              149                168
  N1               58                 75
  N2               18                 22
  N3                2                  3
[1] 4 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   189   1
  10Q LOSS WILD-TYPE 222   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    189    1
  10Q LOSS WILD-TYPE  222    6
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              189                222
  1                1                  6
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    54 175
  10Q LOSS WILD-TYPE  76 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     54  175
  10Q LOSS WILD-TYPE   76  196
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               54                 76
  MALE                175                196
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   183  21
  10Q LOSS WILD-TYPE 201  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    183   21
  10Q LOSS WILD-TYPE  201   32
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO               183                201
  YES               21                 32
[1] 2 2
[1] FALSE
D61V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                       8
  10Q LOSS WILD-TYPE                                     7
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  10Q LOSS MUTATED                                        2
  10Q LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                         0
  10Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                           219
  10Q LOSS WILD-TYPE                                                         260
D61V10, multiclass
                                                             clus
vv                                                            10Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              219
                                                             clus
vv                                                            10Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                260
[1] 4 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   188   4   0  10
  10Q LOSS WILD-TYPE 211   8   4  13
D61V13, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0              188                211
  R1                4                  8
  R2                0                  4
  RX               10                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       3                        18   157
  10Q LOSS WILD-TYPE     6                        13   192
D61V14, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN               18                 13
  WHITE                                  157                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V15, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4 143
  10Q LOSS WILD-TYPE   4 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  143
  10Q LOSS WILD-TYPE    4  174
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              143                174
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    93  75
  11P LOSS WILD-TYPE 187 139
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               168                326 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                75                139 
$`11P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3416 TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 
       12.20       123.19        31.99        48.82        60.66        22.06 
TCGA-33-4533 TCGA-33-6737 TCGA-34-2605 TCGA-43-7657 TCGA-43-A56V TCGA-56-7221 
      133.74        19.76        28.96         7.76        12.03        19.99 
TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 
       16.77        21.04         0.13         9.01        35.34        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-90-7964 TCGA-96-7545 TCGA-98-8020 
       66.61         8.02        42.08        14.07        57.07         2.76 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W 
        0.07        76.80        40.90        65.65        16.80         8.58 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-21-1071 TCGA-21-1076 
       11.34        23.54        36.07        86.96        46.88        60.89 
TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 
      122.43       119.80        43.23        31.63        33.93        10.82 
TCGA-22-1002 TCGA-22-1012 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-5473 
        4.31        14.10        35.08         0.56        34.75        63.55 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 TCGA-33-4538 
       44.25         0.79        86.30        79.20        18.84        97.94 
TCGA-33-4547 TCGA-33-4587 TCGA-33-AASB TCGA-33-AASI TCGA-34-2600 TCGA-34-5231 
       79.53        54.44         6.94        44.19        61.61        65.23 
TCGA-34-5232 TCGA-34-5236 TCGA-34-5928 TCGA-34-5929 TCGA-37-3789 TCGA-37-4130 
       81.24         9.07        39.32         4.96         0.43         8.12 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
        7.46         6.81         0.39       133.25       111.35        68.58 
TCGA-39-5022 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-43-2581 TCGA-43-3920 
       55.20        60.53        68.38        55.56        38.66        33.11 
TCGA-43-6143 TCGA-46-3768 TCGA-46-6025 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 
       22.98         9.83        10.65        18.48        31.27        30.41 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
       17.49         1.35        13.81        20.25        15.81        19.23 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8387 TCGA-58-8390 TCGA-60-2695 TCGA-60-2698 
       18.74        14.47        13.25        29.95        21.11        10.22 
TCGA-60-2708 TCGA-60-2714 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 
       80.45        50.33        35.90        23.57        11.77        52.67 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-66-2742 TCGA-66-2758 TCGA-66-2759 TCGA-66-2767 
       59.97        45.57        21.07        21.01        25.05         2.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2793 
       19.00         3.02        12.03         3.98        12.00        10.06 
TCGA-66-2800 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6844 TCGA-77-7139 
       49.05         6.94        13.35        14.73        75.09       140.09 
TCGA-77-7141 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8133 
        0.49         0.16        32.55        86.76        55.73        53.92 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
       17.72        11.54        26.40        27.39        66.51        54.41 
TCGA-77-8153 TCGA-77-A5G8 TCGA-85-6561 TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 
       65.49        61.94        40.24        36.53        32.91         1.15 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8277 TCGA-85-8288 TCGA-85-8352 TCGA-85-8353 
       18.94        25.15        10.09        13.22         5.29         3.09 
TCGA-85-8479 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
       15.39        34.13        19.86        30.48        19.73        15.85 
TCGA-85-A5B5 TCGA-90-A59Q TCGA-94-8035 TCGA-94-8490 TCGA-94-A5I6 TCGA-98-8023 
        3.65        10.59         4.01         5.03        17.69        21.34 
TCGA-98-A538 TCGA-98-A53J TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HJ 
       27.16        20.71        13.41        11.84        64.54        13.74 
TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V 
       49.28        14.73        83.57        33.07         3.72        43.89 

$`11P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
        4.47         4.80         6.18        27.19        32.19        14.93 
TCGA-22-5472 TCGA-33-4532 TCGA-33-4589 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 
       64.93       129.01         1.55        31.50        31.27        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-8201 
       22.49        18.38        78.18         2.93        11.61        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-60-2696 TCGA-60-2711 TCGA-77-7140 
        3.45        17.00        17.85         3.58        41.42        20.78 
TCGA-77-A5GB TCGA-90-7766 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
       30.81         9.50        21.04         0.16        18.38        16.14 
TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HM TCGA-NK-A7XE 
       19.36         5.69        21.21        19.10        39.85         0.43 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 
       75.75       117.57        92.15        92.42         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
       49.94       119.54        99.16        70.16        34.78        15.58 
TCGA-21-1079 TCGA-21-1081 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 
       31.73         9.34        88.11        41.69        21.99         7.33 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
       64.21         1.74        27.02        20.48        48.33        24.13 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       38.17        13.12        32.02        19.30         9.57        11.77 
TCGA-22-5474 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       14.63        71.34        11.74        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 
       16.64       173.82       103.53       151.27        14.07        63.35 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL 
        4.70         0.30        36.62       110.99       118.36        27.16 
TCGA-34-2596 TCGA-34-2608 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        2.63        32.88        74.66        60.30        50.66        16.93 
TCGA-34-5927 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       44.75         1.12        38.79         4.04        26.43        33.90 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EL 
        4.01         0.39         7.96         7.82         3.39        37.58 
TCGA-37-A5EN TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       21.70       126.58        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 
        1.94        36.39        71.18        17.06        40.21        39.12 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       13.02         4.44        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
       28.34         5.46        30.35         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 
       12.43        18.25        21.90        14.53        19.76         6.51 
TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
        0.10        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-A49D 
       14.07         1.81        22.75        10.36         9.93        20.94 
TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8386 TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 
       13.32         0.26         0.03        13.55        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       34.78        85.12        34.36        56.65        35.24        29.92 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 
       12.23        96.82        37.94        92.71        21.93        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       66.54        56.91        48.49        42.64         3.19        29.85 
TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       26.83        70.13        70.42        68.15        55.30       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       70.62        58.65        14.99        11.34        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        36.16        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       43.10         2.01         0.99         1.02         2.01         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
        0.99        43.99         0.99         2.01         1.02         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 
        7.07        23.01         2.01        19.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       25.97        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I 
       30.02        54.08         4.01         2.73         6.64        16.18 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 
       12.07        12.33        29.56        73.12        23.28        11.18 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 
       73.22        70.13       106.95        46.78         6.51        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8145 TCGA-77-8154 
      156.66        12.59        39.09       104.09         6.97        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       36.36       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 
       27.62        38.86         9.67        41.39         6.41        34.95 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       31.30         1.38        29.95        19.04        24.13        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 
       26.79        30.64        34.52         0.76        22.45        16.77 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
       32.71         2.01         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M 
       18.08        22.59        30.28        30.97        24.36        27.16 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       16.21        14.96        15.29        29.92        12.39        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 
        2.93        11.77        20.22        22.62         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 
        4.01         5.26         2.30        26.63        14.14        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       18.31        17.46        27.68        21.44        30.81        30.67 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
       18.15         2.01        27.02        20.32        18.58        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK 
       16.11        13.18         4.54         1.22        57.30         4.21 
TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52S 
        2.89        43.92        25.32        26.43         3.65        12.72 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            140.09             173.82 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            22.520             21.585 
[1] "0.1 - 140.1 (22.5)" "0.0 - 173.8 (21.6)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         2       27       55        1        21        30
  11P LOSS WILD-TYPE       0       62       97        1        44        65
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  11P LOSS MUTATED           1         23          4        4
  11P LOSS WILD-TYPE         2         40         15        3
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 27                 62
  STAGE IB                 55                 97
  STAGE II                  1                  1
  STAGE IIA                21                 44
  STAGE IIB                30                 65
  STAGE III                 1                  2
  STAGE IIIA               23                 40
  STAGE IIIB                4                 15
  STAGE IV                  4                  3
[1] 10  2
[1] 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    33 103  27   6
  11P LOSS WILD-TYPE  79 191  44  18
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               33                 79
  T2              103                191
  T3               27                 44
  T4                6                 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
  11P LOSS MUTATED   108  50   9   1
  11P LOSS WILD-TYPE 209  83  31   4
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0              108                209
  N1               50                 83
  N2                9                 31
  N3                1                  4
[1] 4 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   140   4
  11P LOSS WILD-TYPE 271   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    140    4
  11P LOSS WILD-TYPE  271    3
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0              140                271
  1                4                  3
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    39 130
  11P LOSS WILD-TYPE  91 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     39  130
  11P LOSS WILD-TYPE   91  241
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               39                 91
  MALE                130                241
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   131  19
  11P LOSS WILD-TYPE 253  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    131   19
  11P LOSS WILD-TYPE  253   34
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO               131                253
  YES               19                 34
[1] 2 2
[1] FALSE
D62V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                       6
  11P LOSS WILD-TYPE                                     9
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  11P LOSS MUTATED                                        1
  11P LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                         1
  11P LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                           161
  11P LOSS WILD-TYPE                                                         318
D62V10, multiclass
                                                             clus
vv                                                            11P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              161
                                                             clus
vv                                                            11P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D62V11, continuous
D62V12, continuous
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED   136   3   1   8
  11P LOSS WILD-TYPE 263   9   3  15
D62V13, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0              136                263
  R1                3                  9
  R2                1                  3
  RX                8                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                        13   122
  11P LOSS WILD-TYPE     8                        18   227
D62V14, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN               13                 18
  WHITE                                  122                227
[1] 3 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     2 111
  11P LOSS WILD-TYPE   6 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2  111
  11P LOSS WILD-TYPE    6  206
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO              111                206
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    78  64
  11Q LOSS WILD-TYPE 202 150
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               142                352 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                64                150 
$`11Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3416 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 
       12.20       123.19        31.99       133.74         1.55        19.76 
TCGA-34-2605 TCGA-43-7657 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8504 
       28.96         7.76        11.61        12.03        19.99        16.77 
TCGA-56-A4ZJ TCGA-60-2712 TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-90-7766 
       21.04         9.01        35.34        66.61         8.02         9.50 
TCGA-90-7964 TCGA-96-7545 TCGA-98-8020 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A5CT 
       14.07        57.07         2.76         0.07        76.80        65.65 
TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
       16.80         8.58        11.34        23.54        36.07        86.96 
TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-21-5783 TCGA-21-5787 TCGA-22-1002 
       60.89       122.43        43.23        88.11        10.82         4.31 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4601 TCGA-22-5473 TCGA-22-5477 
        1.74        14.10        35.08        34.75        63.55        44.25 
TCGA-22-5478 TCGA-33-AASB TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-5232 
        0.79         6.94        27.16         2.63        61.61        81.24 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5928 TCGA-37-3789 TCGA-37-4130 TCGA-39-5016 
        9.07        60.30        39.32         0.43         8.12       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5031 TCGA-39-5037 
      111.35        68.58        55.20       102.18        60.53        55.56 
TCGA-43-2581 TCGA-43-3920 TCGA-43-8116 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       38.66        33.11        11.77         9.83        10.65        13.91 
TCGA-51-4079 TCGA-52-7809 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7822 
        0.39         5.46        18.48        14.53        30.41        17.49 
TCGA-56-8624 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-58-8387 
       13.81        15.81        19.23        13.32        18.74        13.25 
TCGA-58-8390 TCGA-60-2695 TCGA-60-2708 TCGA-60-2714 TCGA-60-2722 TCGA-60-2723 
       29.95        21.11        80.45        50.33        29.85        35.90 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-66-2758 
       26.83        11.77        59.97        45.57        78.28        21.01 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2790 TCGA-66-2793 TCGA-66-2800 TCGA-68-8251 
        2.01         2.01        22.98        10.06        49.05        13.35 
TCGA-68-A59J TCGA-77-7139 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
       14.73       140.09         0.16        32.55        86.76        55.73 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8143 TCGA-77-8144 
      156.66        53.92        39.09        17.72        26.40        27.39 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-85-6561 TCGA-85-6798 
       66.51        54.41        65.49       150.25        40.24         6.41 
TCGA-85-7696 TCGA-85-7699 TCGA-85-8048 TCGA-85-8072 TCGA-85-8277 TCGA-85-8352 
       36.53        32.91        25.15        30.64        10.09         5.29 
TCGA-85-8353 TCGA-85-8479 TCGA-85-8664 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
        3.09        15.39        18.08        19.86        30.48        19.73 
TCGA-85-A5B5 TCGA-90-A59Q TCGA-92-7341 TCGA-94-A5I6 TCGA-96-A4JL TCGA-98-8023 
        3.65        10.59         3.48        17.69        27.68        21.34 
TCGA-98-A538 TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HO 
       27.16        20.71        11.84        64.54        13.74        43.92 
TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A5IB 
       83.57        33.07        43.89        11.18 

$`11Q LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
        4.47         4.80         6.18        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-34-2604 
       48.82        60.66        64.93        22.06       129.01        31.50 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 
       31.27        17.88        22.49        18.38        78.18         2.93 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2696 
       13.05         3.45        17.00        17.85         0.13         3.58 
TCGA-60-2711 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-94-7033 
       41.42        32.32        20.78        42.08        30.81        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D 
        0.16        18.38        16.14        19.36         5.69        21.21 
TCGA-J1-A4AH TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3411 
       19.10        39.85        40.90         0.43        75.75       117.57 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.15        92.42         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       46.88        99.16        70.16        34.78        15.58        31.73 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 
        9.34       119.80        31.63        41.69        33.93        21.99 
TCGA-22-0944 TCGA-22-1005 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
        7.33        64.21        27.02        20.48        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
        0.56        38.17        13.12        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
       11.77        14.63        86.30        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 
       18.84        30.12        62.86        56.32        16.64        97.94 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       79.53       173.82       103.53       151.27        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI 
       63.35         4.70         0.30        36.62       110.99        44.19 
TCGA-33-AASJ TCGA-34-2608 TCGA-34-5231 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 
      118.36        32.88        65.23        74.66        50.66        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       44.75         4.96         1.12        38.79         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
       33.90         4.01         0.39         7.96         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        6.81         0.39         3.39        37.58        21.70       133.25 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
       82.52         1.71        24.33         1.94        36.39        68.38 
TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 
       71.18        17.06        40.21        39.12        27.91        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 
        9.73        14.20        13.32        12.16        13.02         4.44 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
        0.39        29.95        28.34        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7579 TCGA-56-7582 
       28.96        12.43        18.25        21.90        31.27        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 
        6.51         0.10        33.24        14.96         4.93         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 
       26.89        14.07         1.35         1.81        22.75        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
        9.93        20.25        20.94         0.26        14.47         0.03 
TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       13.55        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       56.65        35.24        29.92        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       37.94        92.71        21.93        49.48        66.54        56.91 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2724 TCGA-63-6202 TCGA-63-7020 
       48.49        42.64         3.19        23.57        52.67        70.13 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       70.42        68.15        55.30       102.67        70.62        58.65 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV 
       14.99        11.34        25.28        89.29        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       53.88        34.59        16.96        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        0.99         1.02         2.01         0.92         0.99        43.99 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 
       25.05         0.99         2.01         1.02         7.07        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       19.00         3.02         2.01        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
       12.00        24.95         1.97        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 
        4.04         5.03        30.02        54.08         4.01         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 
        6.64         6.94        16.18        12.07        12.33        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 
       73.12        75.09        23.28        11.18         0.49        73.22 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 
       70.13       106.95        46.78         6.51        37.81        12.59 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
      104.09        11.54         6.97        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH 
      132.36        22.29         5.92        61.94        27.62        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 
        9.67        41.39        34.95        31.30         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       29.95        18.94        19.04        24.13        31.56        26.79 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 
       34.52         0.76        13.22        22.45        16.77        32.71 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 
        2.01         7.76        36.59        38.14        12.59        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z 
       30.28        34.13        30.97        24.36        27.16        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       15.85        14.96        15.29        29.92        12.39        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-8063 
        2.93        11.77        20.22        22.62         2.70         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        5.26         2.30         4.01         5.03        26.63        14.14 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       71.01        18.31        17.46        21.44        30.81        30.67 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
       18.15         2.01        27.02        20.32        18.58        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI 
       16.11        13.18        13.41         4.54         1.22        57.30 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
        4.21         2.89        49.28        25.32        14.73        26.43 
TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-XC-AA0X 
        3.65         3.72        12.72         0.20 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.07               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            156.66             173.82 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            23.260             21.585 
[1] "0.1 - 156.7 (23.3)" "0.0 - 173.8 (21.6)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         2       23       44        1        17        28
  11Q LOSS WILD-TYPE       0       66      108        1        48        67
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  11Q LOSS MUTATED           1         20          4        2
  11Q LOSS WILD-TYPE         2         43         15        5
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 23                 66
  STAGE IB                 44                108
  STAGE II                  1                  1
  STAGE IIA                17                 48
  STAGE IIB                28                 67
  STAGE III                 1                  2
  STAGE IIIA               20                 43
  STAGE IIIB                4                 15
  STAGE IV                  2                  5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q LOSS MUTATED    26  90  20   7
  11Q LOSS WILD-TYPE  86 204  51  17
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               26                 86
  T2               90                204
  T3               20                 51
  T4                7                 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    87  48   6   1
  11Q LOSS WILD-TYPE 230  85  34   4
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               87                230
  N1               48                 85
  N2                6                 34
  N3                1                  4
[1] 4 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   118   2
  11Q LOSS WILD-TYPE 293   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    118    2
  11Q LOSS WILD-TYPE  293    5
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0              118                293
  1                2                  5
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    31 112
  11Q LOSS WILD-TYPE  99 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     31  112
  11Q LOSS WILD-TYPE   99  259
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               31                 99
  MALE                112                259
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   119  11
  11Q LOSS WILD-TYPE 265  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    119   11
  11Q LOSS WILD-TYPE  265   42
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               119                265
  YES               11                 42
[1] 2 2
[1] FALSE
D63V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                       6
  11Q LOSS WILD-TYPE                                     9
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  11Q LOSS MUTATED                                        1
  11Q LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                         0
  11Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                           136
  11Q LOSS WILD-TYPE                                                         343
D63V10, multiclass
                                                             clus
vv                                                            11Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              136
                                                             clus
vv                                                            11Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                343
[1] 4 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   115   2   1   3
  11Q LOSS WILD-TYPE 284  10   3  20
D63V13, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0              115                284
  R1                2                 10
  R2                1                  3
  RX                3                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                        12   101
  11Q LOSS WILD-TYPE     7                        19   248
D63V14, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               12                 19
  WHITE                                  101                248
[1] 3 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  99
  11Q LOSS WILD-TYPE   6 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   99
  11Q LOSS WILD-TYPE    6  218
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               99                218
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    21  18
  12P LOSS WILD-TYPE 259 196
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                39                455 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                18                196 
$`12P LOSS MUTATED`
TCGA-18-3407 TCGA-33-4533 TCGA-34-2604 TCGA-43-5668 TCGA-43-8118 TCGA-77-A5GA 
        4.47       133.74        31.50        18.38         2.93        42.08 
TCGA-22-1016 TCGA-22-5478 TCGA-33-4587 TCGA-33-AASB TCGA-34-A5IX TCGA-37-4129 
       27.02         0.79        54.44         6.94        33.90         7.96 
TCGA-37-4130 TCGA-37-4141 TCGA-37-A5EN TCGA-39-5011 TCGA-43-2581 TCGA-43-6143 
        8.12         0.39        21.70       133.25        38.66        22.98 
TCGA-56-5898 TCGA-56-7579 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4ZK TCGA-60-2722 
       18.25        31.27        13.81        20.94        18.74        29.85 
TCGA-66-2773 TCGA-77-7138 TCGA-77-8008 TCGA-77-8150 TCGA-77-8153 TCGA-85-6798 
        3.02        11.18        86.76        54.41        65.49         6.41 
TCGA-85-8353 TCGA-85-8479 TCGA-85-A4JB TCGA-85-A50M TCGA-85-A5B5 TCGA-90-A4ED 
        3.09        15.39        30.97        27.16         3.65        20.22 
TCGA-NC-A5HL TCGA-NK-A5CR TCGA-O2-A52V 
        2.89        83.57        43.89 

$`12P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20       123.19         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 
      129.01         1.55        19.76        28.96        31.27        17.88 
TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       22.49         7.76        78.18        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ 
       13.05         3.45        17.00        16.77        17.85        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 
        0.13         3.58        41.42         9.01        35.34        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
       66.61         8.02        20.78        30.81         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       21.04         0.16        18.38        16.14        57.07        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE 
        2.76         5.69        21.21        19.10         0.07        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
       39.85        40.90        65.65        16.80         0.43         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
       75.75       117.57        11.34        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.42        86.96         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       46.88        99.16        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       31.73       122.43         9.34       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
       88.11        41.69        33.93        10.82        21.99         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
        4.31        64.21         1.74        14.10        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       48.33        24.13         0.56        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       32.02        19.30         9.57        11.77        63.55        14.63 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       44.25        86.30        71.34        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 
       30.12        62.86        56.32        16.64        97.94        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN 
      173.82       103.53       151.27        14.07        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
        0.30        36.62       110.99        44.19       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        2.63        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        60.30        50.66        16.93        44.75        39.32 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 
        4.96         1.12        38.79         4.04        26.43         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 
        0.43         0.39         7.46         7.82         6.81         3.39 
TCGA-37-A5EL TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
       37.58       126.58       111.35        68.58        55.20        82.52 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
      102.18         1.71        24.33         1.94        60.53        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 
       68.38        71.18        55.56        17.06        40.21        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       33.11        27.91        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
       19.59        13.38        11.77         9.73        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       12.16        13.02         9.83         4.44        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
        0.39         0.39        29.95        28.34         5.46        30.35 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 
        8.75        27.45        28.96        12.43        21.90        18.48 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
       14.53        30.41        19.76         6.51         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       33.24        14.96         4.93         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.35         1.81        22.75        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       15.81        19.23        13.32         0.26        14.47         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.25        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       85.12        34.36        56.65        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       12.23        10.22        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       80.45        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       42.64         3.19        35.90        23.57        26.83        11.77 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       52.67        70.13        70.42        68.15        55.30       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       70.62        58.65        59.97        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       25.28        89.29        78.28        16.37        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       34.59        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        1.02         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       25.05         0.99         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        7.07        23.01        19.00         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        3.98        12.00        24.95         1.97        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
       22.98         4.04        22.98         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       54.08         4.01        49.05         2.73         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 
       13.35        16.18        14.73        12.07        12.33        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       73.12        75.09        23.28       140.09         0.49        73.22 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       70.13       106.95         0.16        46.78        32.55         6.51 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       55.73        37.81       156.66        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       17.72       104.09        11.54        26.40        27.39         6.97 
TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       66.51        60.53        36.36       126.18       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       22.29         5.92        61.94        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       41.39        40.24        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        1.38         1.15        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       24.13        31.56        26.79        30.64        34.52        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
        0.76        13.22        22.45        16.77         5.29        32.71 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        2.01         7.76        36.59        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       22.59        30.28        34.13        19.86        24.36        30.48 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       19.73        16.21        15.85        14.96        15.29        29.92 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
       12.39        24.92         2.93        11.77        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
        2.70         3.48         4.01         5.26         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        5.03        26.63        14.14        17.69        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       27.16        18.15         2.01        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        64.54         1.22        57.30        13.74         4.21 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX 
       49.28        43.92        25.32        14.73        26.43         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         3.72        12.72        11.18         0.20 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.39               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            133.74             173.82 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             20.94              21.93 
[1] "0.4 - 133.7 (20.9)" "0.0 - 173.8 (21.9)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         0        8       16        1         3         4
  12P LOSS WILD-TYPE       2       81      136        1        62        91
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  12P LOSS MUTATED           0          6          1        0
  12P LOSS WILD-TYPE         3         57         18        7
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  8                 81
  STAGE IB                 16                136
  STAGE II                  1                  1
  STAGE IIA                 3                 62
  STAGE IIB                 4                 91
  STAGE III                 0                  3
  STAGE IIIA                6                 57
  STAGE IIIB                1                 18
  STAGE IV                  0                  7
[1] 10  2
[1] 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     9  20   9   1
  12P LOSS WILD-TYPE 103 274  62  23
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                9                103
  T2               20                274
  T3                9                 62
  T4                1                 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                  N0  N1  N2  N3
  12P LOSS MUTATED    30   7   2   0
  12P LOSS WILD-TYPE 287 126  38   5
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               30                287
  N1                7                126
  N2                2                 38
  N3                0                  5
[1] 4 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    32   0
  12P LOSS WILD-TYPE 379   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     32    0
  12P LOSS WILD-TYPE  379    7
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               32                379
  1                0                  7
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    11  28
  12P LOSS WILD-TYPE 119 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     11   28
  12P LOSS WILD-TYPE  119  343
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               11                119
  MALE                 28                343
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    33   2
  12P LOSS WILD-TYPE 351  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     33    2
  12P LOSS WILD-TYPE  351   51
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                33                351
  YES                2                 51
[1] 2 2
[1] FALSE
D64V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                       1
  12P LOSS WILD-TYPE                                    14
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  12P LOSS MUTATED                                        1
  12P LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                         1
  12P LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                            36
  12P LOSS WILD-TYPE                                                         443
D64V10, multiclass
                                                             clus
vv                                                            12P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               36
                                                             clus
vv                                                            12P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                443
[1] 4 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    30   1   0   1
  12P LOSS WILD-TYPE 369  11   4  22
D64V13, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               30                369
  R1                1                 11
  R2                0                  4
  RX                1                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       2                         3    26
  12P LOSS WILD-TYPE     7                        28   323
D64V14, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                   26                323
[1] 3 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     0  30
  12P LOSS WILD-TYPE   8 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   30
  12P LOSS WILD-TYPE    8  287
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               30                287
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    27  19
  12Q LOSS WILD-TYPE 253 195
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                46                448 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                19                195 
$`12Q LOSS MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-33-4533 TCGA-34-2604 TCGA-43-5668 TCGA-43-8118 
        4.47       123.19       133.74        31.50        18.38         2.93 
TCGA-43-A56V TCGA-77-A5GA TCGA-O2-A52W TCGA-18-3408 TCGA-22-4595 TCGA-22-5478 
       12.03        42.08         8.58        75.75        24.13         0.79 
TCGA-33-4587 TCGA-34-A5IX TCGA-37-4129 TCGA-37-4141 TCGA-37-A5EN TCGA-43-2581 
       54.44        33.90         7.96         0.39        21.70        38.66 
TCGA-43-6143 TCGA-51-4081 TCGA-52-7810 TCGA-56-5898 TCGA-56-8624 TCGA-56-A49D 
       22.98        29.95        30.35        18.25        13.81        20.94 
TCGA-60-2703 TCGA-60-2722 TCGA-60-2723 TCGA-66-2773 TCGA-77-7138 TCGA-77-8007 
       96.82        29.85        35.90         3.02        11.18         6.51 
TCGA-77-8008 TCGA-77-8131 TCGA-77-8153 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
       86.76        12.59        65.49        41.39         6.41        36.53 
TCGA-85-8479 TCGA-85-A4JB TCGA-85-A50M TCGA-90-A4ED TCGA-94-A4VJ TCGA-94-A5I6 
       15.39        30.97        27.16        20.22        14.14        17.69 
TCGA-98-A53J TCGA-MF-A522 TCGA-NK-A5CR TCGA-O2-A52V 
       20.71        11.84        83.57        43.89 

$`12Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
       12.20         4.80        31.99         6.18        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       14.93        48.82        60.66        64.93        22.06       129.01 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 
        1.55        19.76        28.96        31.27        17.88        22.49 
TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
        7.76        78.18        11.61        19.99        13.05         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       17.00        16.77        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 
       41.42         9.01        35.34        32.32        66.61         8.02 
TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       20.78        30.81         9.50        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
       18.38        16.14        57.07        19.36         2.76         5.69 
TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
       21.21        19.10         0.07        76.80        39.85        40.90 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       65.65        16.80         0.43       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       92.15        36.07        92.42        86.96         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
       49.94       119.54        46.88        99.16        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       34.78        15.58        31.73       122.43         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
       43.23        31.63        88.11        41.69        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       21.99         7.33         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       27.02        20.48        35.08        48.33         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       34.75        13.12        32.02        19.30         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       63.55        14.63        44.25        86.30        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       11.74        18.84        30.12        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       97.94        79.53       173.82       103.53       151.27        14.07 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       63.35         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
       44.19       118.36        27.16         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        81.24        74.66         9.07        60.30        50.66 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        44.75        39.32         4.96         1.12        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 
        4.04        26.43         4.01         0.43         0.39         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 
        7.46         7.82         6.81         3.39        37.58       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1.71        24.33         1.94        60.53        36.39        68.38 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 
       71.18        55.56        17.06        40.21        39.12        33.11 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       13.02         9.83         4.44        10.65        13.91         0.39 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
        0.39        28.34         5.46         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       12.43        21.90        18.48        14.53        31.27        30.41 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       19.76         6.51         0.10        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        4.93         3.48        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
       22.75        10.36         9.93        20.25        15.81        19.23 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       13.32        18.74         0.26        14.47         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       13.55        29.95        71.24        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       34.36        56.65        35.24        29.92        21.11        12.23 
TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       10.22        37.94        92.71        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       66.54        56.91        50.33        48.49        42.64         3.19 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
       23.57        26.83        11.77        52.67        70.13        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       68.15        55.30       102.67        70.62        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       45.57        14.99        11.34        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       16.37        36.16        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
        2.01        21.07         0.99         1.02         2.01         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.99        43.99        21.01        25.05         0.99         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
        1.02         2.01         2.01         7.07        23.01        19.00 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        2.01        19.00        12.03         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1.97        25.97        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         6.94        13.35        16.18        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        29.56        73.12        75.09        23.28 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 
       46.78        32.55        55.73        37.81       156.66        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       39.09        17.72       104.09        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        6.97        66.51        54.41        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      132.36       150.25        22.29         5.92        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       38.86         9.67        40.24        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        1.38         1.15        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       24.13        31.56        26.79        30.64        34.52        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
        0.76        13.22        22.45        16.77         5.29         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
       32.71         2.01         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA 
       18.08        22.59        30.28        34.13        19.86        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
       30.48        19.73        16.21        15.85        14.96        15.29 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
       29.92        12.39         3.65        24.92         2.93        11.77 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       22.62        10.59         2.70         3.48         4.01         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-8169 
        2.30         4.01         5.03        26.63        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       27.16        18.15         2.01        27.02        20.32        18.58 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG 
       12.89        16.11        13.18        13.41         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
        1.22        57.30        13.74         4.21         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52N 
       43.92        25.32        14.73        26.43         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        12.72        11.18         0.20 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.39               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            133.74             173.82 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            22.340             21.685 
[1] "0.4 - 133.7 (22.3)" "0.0 - 173.8 (21.7)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         1        8       18        1         3        10
  12Q LOSS WILD-TYPE       1       81      134        1        62        85
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  12Q LOSS MUTATED           0          5          1        0
  12Q LOSS WILD-TYPE         3         58         18        7
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  8                 81
  STAGE IB                 18                134
  STAGE II                  1                  1
  STAGE IIA                 3                 62
  STAGE IIB                10                 85
  STAGE III                 0                  3
  STAGE IIIA                5                 58
  STAGE IIIB                1                 18
  STAGE IV                  0                  7
[1] 10  2
[1] 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    10  27   9   1
  12Q LOSS WILD-TYPE 102 267  62  23
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               10                102
  T2               27                267
  T3                9                 62
  T4                1                 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                  N0  N1  N2  N3
  12Q LOSS MUTATED    33   9   4   0
  12Q LOSS WILD-TYPE 284 124  36   5
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               33                284
  N1                9                124
  N2                4                 36
  N3                0                  5
[1] 4 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    38   0
  12Q LOSS WILD-TYPE 373   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     38    0
  12Q LOSS WILD-TYPE  373    7
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               38                373
  1                0                  7
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    14  33
  12Q LOSS WILD-TYPE 116 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     14   33
  12Q LOSS WILD-TYPE  116  338
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               14                116
  MALE                 33                338
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    38   3
  12Q LOSS WILD-TYPE 346  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     38    3
  12Q LOSS WILD-TYPE  346   50
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                38                346
  YES                3                 50
[1] 2 2
[1] FALSE
D65V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED                                       2
  12Q LOSS WILD-TYPE                                    13
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  12Q LOSS MUTATED                                        1
  12Q LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED                                         1
  12Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                            43
  12Q LOSS WILD-TYPE                                                         436
D65V10, multiclass
                                                             clus
vv                                                            12Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               43
                                                             clus
vv                                                            12Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                436
[1] 4 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    32   0   0   3
  12Q LOSS WILD-TYPE 367  12   4  20
D65V13, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               32                367
  R1                0                 12
  R2                0                  4
  RX                3                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       2                         4    31
  12Q LOSS WILD-TYPE     7                        27   318
D65V14, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                4                 27
  WHITE                                   31                318
[1] 3 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     0  35
  12Q LOSS WILD-TYPE   8 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   35
  12Q LOSS WILD-TYPE    8  282
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               35                282
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   181 125
  13Q LOSS WILD-TYPE  99  89
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               306                188 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               125                 89 
$`13Q LOSS MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1017 
      123.19         4.80        31.99         6.18        32.19        48.82 
TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       60.66        64.93        22.06         1.55        19.76        31.50 
TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 TCGA-43-A474 
       28.96        31.27        22.49        18.38        78.18        11.61 
TCGA-56-8308 TCGA-56-A4BY TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 
       17.00        17.85         3.58        41.42         9.01        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 
       66.61         8.02        20.78        42.08         9.50        14.07 
TCGA-94-7557 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-J1-A4AH 
        0.16        16.14        57.07        19.36         5.69        19.10 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3415 
        0.07        76.80        39.85        65.65        16.80        92.15 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
       92.42        86.96       154.32       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
       70.16        60.89       122.43        43.23        33.93        10.82 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       21.99         4.31         1.74        27.02        20.48        35.08 
TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
        0.56        34.75        13.12        32.02        19.30        11.77 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       63.55        44.25         0.79        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 
       30.12        56.32        16.64        97.94       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       14.07        54.44        63.35         4.70         0.30        36.62 
TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       44.19         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-3792 TCGA-37-4129 
       39.32         4.96         1.12        26.43         0.39         7.96 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
        7.46         7.82         6.81         3.39       133.25       126.58 
TCGA-39-5022 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 
       55.20         1.71        24.33         1.94        60.53        71.18 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       38.66        39.12        33.11        22.98        24.89        21.47 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       19.59        13.38        11.77        13.32        12.16        13.02 
TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 
        4.44        10.65         0.39        28.34         5.46         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
       27.45        28.96        18.48        31.27        19.76         6.51 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8624 
       33.24        14.96         3.48        26.89        14.07        13.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A62T 
       10.36         9.93        20.25        15.81        20.94        14.47 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
        0.03        13.25        29.95        71.24        34.78        85.12 
TCGA-58-A46K TCGA-58-A46M TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       34.36        35.24        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
       80.45        66.54        56.91        50.33        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       29.85        35.90        23.57        26.83        11.77        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       70.13        70.42        68.15       102.67        70.62        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       59.97        45.57        11.34        25.28        89.29        78.28 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 
       53.88        34.59        16.96        43.10         1.02         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 
        0.92         0.99        21.01        25.05         0.99         2.01 
TCGA-66-2768 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        2.01        19.00         2.01        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
       12.00        24.95         1.97        25.97        40.01        22.98 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       22.98        30.02        49.05         2.73         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 
       13.35        16.18        29.56        75.09       140.09         0.49 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       70.13       106.95         0.16        46.78        32.55         6.51 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 
       55.73       156.66        12.59        53.92        17.72       104.09 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       26.40        27.39        66.51        54.41        65.49        60.53 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      132.36       150.25        22.29         5.92        61.94        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7844 TCGA-85-7950 
        9.67        40.24        34.95        31.30        29.95        18.94 
TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       19.04        31.56        26.79        10.09         0.76        13.22 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8580 TCGA-85-8664 TCGA-85-A4CN 
       16.77         5.29         3.09        36.59        18.08        34.13 
TCGA-85-A4JB TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A53L 
       30.97        19.73        16.21        15.85        15.29        12.39 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 
        3.65         2.93        11.77        22.62         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-94-8035 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.26         4.01        26.63        17.69        71.01 
TCGA-96-8169 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       18.31        21.44        30.81        30.67        21.34        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 
       18.15         2.01        18.58        20.71        12.89        16.11 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54        64.54        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       49.28        43.92        25.32        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        3.65         3.72        12.72        43.89        11.18         0.20 

$`13Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-5595 TCGA-22-1000 TCGA-33-4532 TCGA-33-4533 
       12.20         4.47        27.19        14.93       129.01       133.74 
TCGA-39-5039 TCGA-43-7657 TCGA-43-8118 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 
       17.88         7.76         2.93        12.03        19.99        13.05 
TCGA-56-8305 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2715 TCGA-77-A5GB 
        3.45        16.77        21.04         0.13        35.34        30.81 
TCGA-94-7033 TCGA-94-7943 TCGA-98-8020 TCGA-98-A53D TCGA-NC-A5HR TCGA-NK-A7XE 
       21.04        18.38         2.76        21.21        40.90         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 
        8.58        75.75       117.57        11.34        23.54        36.07 
TCGA-18-4086 TCGA-18-5592 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
        2.79        49.94        34.78        15.58        31.73         9.34 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0944 TCGA-22-1005 
      119.80        31.63        88.11        41.69         7.33        64.21 
TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4609 TCGA-22-5474 
       14.10        48.33        24.13        38.17         9.57        14.63 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5489 TCGA-33-4547 TCGA-33-4566 TCGA-33-AASB 
       86.30        71.34        62.86        79.53       173.82         6.94 
TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
      110.99       118.36        27.16        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX 
       50.66        16.93        44.75        38.79         4.04        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN 
        4.01         0.43         8.12         0.39        37.58        21.70 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 
      111.35        68.58        82.52       102.18        36.39        68.38 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-5670 TCGA-43-6771 TCGA-43-6773 
       55.56        17.06        40.21        27.91         5.46         3.81 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 
        9.73        14.20         9.83        13.91         0.39        29.95 
TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7580 
       30.35        12.43        18.25        21.90        14.53        30.41 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8083 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        0.10        17.49         4.93         1.35         1.81        22.75 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8392 
       19.23        13.32        18.74         0.26        13.55        16.47 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2709 
       56.65        29.92        21.11        12.23        10.22        49.48 
TCGA-60-2716 TCGA-63-7023 TCGA-63-A5MM TCGA-63-A5MT TCGA-63-A5MV TCGA-66-2737 
       48.49        55.30        14.99        16.37        36.16         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 
       21.07         0.99        43.99         2.01         1.02         7.07 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 
       23.01         3.02         4.04         5.03        10.06        54.08 
TCGA-66-2795 TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6843 TCGA-77-6845 
        4.01        14.73        12.07        12.33        73.12        23.28 
TCGA-77-7138 TCGA-77-7142 TCGA-77-8008 TCGA-77-8128 TCGA-77-8136 TCGA-77-8140 
       11.18        73.22        86.76        37.81        39.09        11.54 
TCGA-77-8145 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        6.97        36.36       126.18        38.86        41.39         6.41 
TCGA-85-7696 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8052 
       36.53        32.91         1.38         1.15        25.15        24.13 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8350 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       30.64        34.52        22.45        32.71         2.01        15.39 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC 
        7.76        38.14        12.59        22.59        30.28        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 
       24.36        30.48        27.16        14.96        29.92        24.92 
TCGA-90-A4ED TCGA-90-A59Q TCGA-92-8065 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-8170 
       20.22        10.59         2.30         5.03        14.14        17.46 
TCGA-96-A4JL TCGA-98-A53C TCGA-98-A53H TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       27.68        27.02        20.32        13.18        13.41        11.84 
TCGA-NC-A5HH TCGA-O2-A52N 
        1.22        33.07 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.03               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            156.66             173.82 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             22.80              20.68 
[1] "0.0 - 156.7 (22.8)" "0.1 - 173.8 (20.7)"
[1] "hr=" "1.3"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         0       52       91        2        45        62
  13Q LOSS WILD-TYPE       2       37       61        0        20        33
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  13Q LOSS MUTATED           3         41          8        3
  13Q LOSS WILD-TYPE         0         22         11        4
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 52                 37
  STAGE IB                 91                 61
  STAGE II                  2                  0
  STAGE IIA                45                 20
  STAGE IIB                62                 33
  STAGE III                 3                  0
  STAGE IIIA               41                 22
  STAGE IIIB                8                 11
  STAGE IV                  3                  4
[1] 10  2
[1] 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    68 190  42  11
  13Q LOSS WILD-TYPE  44 104  29  13
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               68                 44
  T2              190                104
  T3               42                 29
  T4               11                 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
  13Q LOSS MUTATED   190  91  24   3
  13Q LOSS WILD-TYPE 127  42  16   2
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0              190                127
  N1               91                 42
  N2               24                 16
  N3                3                  2
[1] 4 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   259   3
  13Q LOSS WILD-TYPE 152   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    259    3
  13Q LOSS WILD-TYPE  152    4
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0              259                152
  1                3                  4
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    82 229
  13Q LOSS WILD-TYPE  48 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     82  229
  13Q LOSS WILD-TYPE   48  142
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               82                 48
  MALE                229                142
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   245  33
  13Q LOSS WILD-TYPE 139  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    245   33
  13Q LOSS WILD-TYPE  139   20
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               245                139
  YES               33                 20
[1] 2 2
[1] FALSE
D66V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                       7
  13Q LOSS WILD-TYPE                                     8
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  13Q LOSS MUTATED                                        0
  13Q LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                         1
  13Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                           303
  13Q LOSS WILD-TYPE                                                         176
D66V10, multiclass
                                                             clus
vv                                                            13Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              303
                                                             clus
vv                                                            13Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                176
[1] 4 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   246   7   3  16
  13Q LOSS WILD-TYPE 153   5   1   7
D66V13, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0              246                153
  R1                7                  5
  R2                3                  1
  RX               16                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       2                        18   216
  13Q LOSS WILD-TYPE     7                        13   133
D66V14, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               18                 13
  WHITE                                  216                133
[1] 3 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     8 183
  13Q LOSS WILD-TYPE   0 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8  183
  13Q LOSS WILD-TYPE    0  134
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  0
  NOT HISPANIC OR LATINO              183                134
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    89  76
  14Q LOSS WILD-TYPE 191 138
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               165                329 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                76                138 
$`14Q LOSS MUTATED`
TCGA-18-3410 TCGA-18-4083 TCGA-34-2604 TCGA-34-2605 TCGA-43-7657 TCGA-43-7658 
        4.80         6.18        31.50        28.96         7.76        78.18 
TCGA-56-8201 TCGA-56-8305 TCGA-56-A4BY TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 
       13.05         3.45        17.85         9.01        66.61         8.02 
TCGA-90-7766 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-NC-A5HD 
        9.50         0.16        18.38        16.14        57.07         0.07 
TCGA-NC-A5HE TCGA-NK-A5CT TCGA-18-4086 TCGA-21-1071 TCGA-21-1083 TCGA-21-5784 
       76.80        65.65         2.79        46.88        43.23        41.69 
TCGA-22-0940 TCGA-22-1012 TCGA-22-1016 TCGA-22-4596 TCGA-22-4601 TCGA-22-4613 
       21.99        14.10        27.02         0.56        34.75        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 
       63.55        14.63        44.25        71.34        79.20        18.84 
TCGA-22-5491 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW 
       56.32       151.27        14.07        54.44         4.70         0.30 
TCGA-33-AAS8 TCGA-34-2596 TCGA-34-2600 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       36.62         2.63        61.61        44.75        39.32         4.96 
TCGA-34-A5IX TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-A5EL TCGA-37-A5EN 
       33.90         8.12         7.82         6.81        37.58        21.70 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 
      126.58        68.58        82.52         1.94        68.38        17.06 
TCGA-43-3394 TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 TCGA-43-A475 TCGA-46-3768 
       39.12        21.47        19.59        11.77         9.73         9.83 
TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 TCGA-56-5897 TCGA-56-7582 TCGA-56-8082 
       13.91         0.39         5.46        12.43        19.76        14.96 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       26.89        14.07         1.35        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-A46J TCGA-58-A46K TCGA-60-2695 TCGA-60-2704 TCGA-60-2709 
       71.24        85.12        34.36        21.11        37.94        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
       66.54        56.91        50.33        35.90        26.83        11.77 
TCGA-63-6202 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MW 
       52.67        55.30       102.67        45.57        25.28        53.88 
TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
       16.96         1.02         2.01         0.92        43.99        21.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2786 TCGA-66-2787 TCGA-66-2795 
        7.07        23.01         3.02        25.97        40.01         4.01 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-7139 
        6.94        13.35        14.73        29.56        73.12       140.09 
TCGA-77-7141 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8140 
        0.49         0.16        32.55        86.76        55.73        11.54 
TCGA-77-8156 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
       36.36         5.92        27.62        38.86        41.39         6.41 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1.15        29.95        18.94        25.15        19.04        24.13 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8352 
       31.56        30.64        10.09         0.76        13.22         5.29 
TCGA-85-8580 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A510 
       36.59        18.08        30.28        34.13        19.86        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
       14.96        15.29        29.92         2.93        11.77        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-94-A5I6 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       22.62        10.59        17.69        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53J TCGA-LA-A446 TCGA-NC-A5HJ 
       30.67        21.34        18.15        20.71        13.18        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-XC-AA0X 
        4.21         2.89         0.20 

$`14Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI 
       12.20         4.47       123.19        31.99        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       14.93        48.82        60.66        64.93        22.06       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 
      133.74         1.55        19.76        31.27        17.88        22.49 
TCGA-43-5668 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8308 
       18.38         2.93        11.61        12.03        19.99        17.00 
TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 
       16.77        21.04         0.13         3.58        41.42        35.34 
TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 
       32.32        20.78        42.08        30.81        14.07        21.04 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HM 
       19.36         2.76         5.69        21.21        19.10        39.85 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       40.90        16.80         0.43         8.58        75.75       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       11.34        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
      154.32        49.94       119.54        99.16        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       34.78        15.58        31.73       122.43         9.34       119.80 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 
       31.63        88.11        33.93        10.82         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
       64.21         1.74        20.48        35.08        48.33        24.13 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5478 
       38.17        13.12        32.02        19.30         9.57         0.79 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 
       86.30        11.74        30.12        62.86        16.64        97.94 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-6738 TCGA-33-AASB TCGA-33-AASD 
       79.53       173.82       103.53        63.35         6.94       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       44.19       118.36        27.16        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-7107 
       74.66         9.07        60.30        50.66        16.93         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       38.79         4.04        26.43         4.01         0.43         0.39 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 
        7.96         7.46         0.39         3.39       133.25       111.35 
TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 
       55.20       102.18         1.71        24.33        60.53        36.39 
TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 
       71.18        55.56        40.21        38.66        33.11        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-A56U 
       22.98        24.89         5.46         3.81        13.38        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6025 TCGA-51-4080 
       13.32        12.16        13.02         4.44        10.65         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
       29.95        28.34        30.35         8.75        27.45        28.96 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       18.25        21.90        18.48        14.53        31.27        30.41 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 
        6.51         0.10        17.49        33.24         4.93         3.48 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75        13.81        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
       15.81        20.94        19.23        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M 
       14.47         0.03        16.47        34.78        56.65        35.24 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
       29.92        12.23        10.22        96.82        92.71        21.93 
TCGA-60-2708 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2724 
       80.45        48.49        42.64         3.19        29.85        23.57 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       70.13        70.42        68.15        70.62        58.65        59.97 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       14.99        11.34        89.29        78.28        16.37        36.16 
TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 
       34.59        43.10         2.01        21.07         0.99         0.99 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       25.05         0.99         2.01         1.02         2.01         2.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
       19.00         2.01        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       24.95         1.97        22.98         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       30.02        10.06        54.08        49.05         2.73         6.64 
TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       16.18        12.07        12.33        75.09        23.28        11.18 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 
       73.22        70.13       106.95        46.78         6.51        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
      156.66        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       26.40        27.39         6.97        66.51        54.41        65.49 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 
       60.53       126.18       132.36       150.25        22.29        61.94 
TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
        9.67        40.24        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-8071 TCGA-85-8276 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
        1.38        26.79        34.52        22.45        16.77         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 
       32.71         2.01        15.39         7.76        38.14        12.59 
TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       22.59        30.97        24.36        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-92-7340 TCGA-92-7341 
       16.21        12.39         3.65        24.92         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         5.26         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-A538 TCGA-98-A53B 
       14.14        71.01        18.31        17.46        27.16         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW 
       27.02        20.32        18.58        12.89        16.11        13.41 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HN 
       11.84         4.54        64.54         1.22        57.30        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
       43.92        25.32        14.73        26.43        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       33.07         3.72        12.72        43.89        11.18 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            151.27             173.82 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             20.71              22.59 
[1] "0.1 - 151.3 (20.7)" "0.0 - 173.8 (22.6)"
[1] "hr=" "1.3"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         0       37       53        0        24        34
  14Q LOSS WILD-TYPE       2       52       99        2        41        61
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  14Q LOSS MUTATED           0         14          4        0
  14Q LOSS WILD-TYPE         3         49         15        7
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 37                 52
  STAGE IB                 53                 99
  STAGE II                  0                  2
  STAGE IIA                24                 41
  STAGE IIB                34                 61
  STAGE III                 0                  3
  STAGE IIIA               14                 49
  STAGE IIIB                4                 15
  STAGE IV                  0                  7
[1] 10  2
[1] 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    47  96  18   6
  14Q LOSS WILD-TYPE  65 198  53  18
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               47                 65
  T2               96                198
  T3               18                 53
  T4                6                 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
  14Q LOSS MUTATED   110  47   8   0
  14Q LOSS WILD-TYPE 207  86  32   5
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              110                207
  N1               47                 86
  N2                8                 32
  N3                0                  5
[1] 4 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   140   0
  14Q LOSS WILD-TYPE 271   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    140    0
  14Q LOSS WILD-TYPE  271    7
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              140                271
  1                0                  7
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    46 121
  14Q LOSS WILD-TYPE  84 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     46  121
  14Q LOSS WILD-TYPE   84  250
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               46                 84
  MALE                121                250
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   129  16
  14Q LOSS WILD-TYPE 255  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    129   16
  14Q LOSS WILD-TYPE  255   37
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               129                255
  YES               16                 37
[1] 2 2
[1] FALSE
D67V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED                                       5
  14Q LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  14Q LOSS MUTATED                                        0
  14Q LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED                                         1
  14Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                           161
  14Q LOSS WILD-TYPE                                                         318
D67V10, multiclass
                                                             clus
vv                                                            14Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              161
                                                             clus
vv                                                            14Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D67V11, continuous
D67V12, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED   137   3   1   5
  14Q LOSS WILD-TYPE 262   9   3  18
D67V13, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0              137                262
  R1                3                  9
  R2                1                  3
  RX                5                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       3                         9   125
  14Q LOSS WILD-TYPE     6                        22   224
D67V14, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                9                 22
  WHITE                                  125                224
[1] 3 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     1 113
  14Q LOSS WILD-TYPE   7 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1  113
  14Q LOSS WILD-TYPE    7  204
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO              113                204
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    73  67
  15Q LOSS WILD-TYPE 207 147
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               140                354 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                67                147 
$`15Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3416 TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-33-4533 
       12.20        31.99        14.93        48.82        60.66       133.74 
TCGA-33-4589 TCGA-43-2578 TCGA-43-5668 TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 
        1.55        22.49        18.38        12.03        13.05         3.45 
TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-96-A4JK TCGA-NC-A5HD TCGA-NC-A5HM 
        9.01        66.61         8.02        19.36         0.07        39.85 
TCGA-O2-A52W TCGA-18-3412 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        8.58        11.34        49.94       119.54        46.88        99.16 
TCGA-21-1080 TCGA-21-5787 TCGA-22-0944 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 
      122.43        10.82         7.33        14.10        27.02        48.33 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-5480 TCGA-33-4582 TCGA-33-4587 
       24.13         0.56        38.17        71.34       103.53        54.44 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2600 TCGA-34-5929 
       36.62       110.99        44.19       118.36        61.61         4.96 
TCGA-34-8456 TCGA-37-3783 TCGA-37-4130 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 
       26.43         4.01         8.12         7.82         0.39         3.39 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
      133.25       126.58        68.58         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5040 TCGA-43-2581 TCGA-43-5670 TCGA-46-3768 
       60.53        36.39        17.06        38.66        27.91         9.83 
TCGA-46-6025 TCGA-46-6026 TCGA-52-7810 TCGA-56-7223 TCGA-56-7580 TCGA-56-7822 
       10.65        13.91        30.35        14.53        30.41        17.49 
TCGA-56-8304 TCGA-56-8309 TCGA-56-8503 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A62T 
        3.48        14.07         1.35        20.94        19.23        14.47 
TCGA-58-8386 TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 TCGA-60-2714 TCGA-60-2720 
        0.03        10.22        96.82        80.45        50.33         3.19 
TCGA-60-2723 TCGA-60-2726 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML 
       35.90        11.77        68.15       102.67        59.97        45.57 
TCGA-63-A5MS TCGA-63-A5MW TCGA-66-2737 TCGA-66-2742 TCGA-66-2756 TCGA-66-2791 
       78.28        53.88         2.01        21.07         0.99         5.03 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
       10.06        54.08        49.05        16.18        14.73        12.07 
TCGA-77-6842 TCGA-77-7139 TCGA-77-7337 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 
       29.56       140.09       106.95         6.51        55.73        37.81 
TCGA-77-8130 TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5GH 
      156.66         6.97        65.49        36.36        22.29        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-7843 TCGA-85-8072 TCGA-85-8288 TCGA-85-8479 
        9.67        41.39         1.15        30.64        13.22        15.39 
TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 
       22.59        30.48        27.16        14.96        12.39         3.65 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 TCGA-94-8491 
        2.93        20.22        22.62         5.26         2.30        26.63 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL 
       11.84         4.54        64.54        57.30         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       49.28        25.32        14.73        83.57         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A5IB 
        3.72        11.18 

$`15Q LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
        4.47       123.19         4.80         6.18        27.19        32.19 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
       64.93        22.06       129.01        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
       31.27        17.88         7.76        78.18         2.93        11.61 
TCGA-56-7221 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
       19.99        17.00        16.77        17.85        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA 
        3.58        41.42        35.34        32.32        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       30.81         9.50        14.07        21.04         0.16        18.38 
TCGA-94-A5I4 TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH 
       16.14        57.07         2.76         5.69        21.21        19.10 
TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 
       76.80        40.90        65.65        16.80         0.43        75.75 
TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
      117.57        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        2.79       154.32        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       31.73         9.34       119.80        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       41.69        33.93        21.99         4.31        64.21         1.74 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       20.48        35.08        34.75        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       86.30        79.20        11.74        18.84        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
       56.32        16.64        97.94        79.53       173.82       151.27 
TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASL 
       14.07        63.35         4.70         0.30         6.94        27.16 
TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
        2.63        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 
       60.30        50.66        16.93        44.75        39.32         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       38.79         4.04        33.90         0.43         0.39         7.96 
TCGA-37-4132 TCGA-37-4135 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5019 TCGA-39-5022 
        7.46         6.81        37.58        21.70       111.35        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
       82.52       102.18        68.38        71.18        55.56        40.21 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       39.12        33.11        22.98        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        3.81        19.59        13.38        11.77         9.73        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-51-4079 TCGA-51-4080 
       13.32        12.16        13.02         4.44         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
       29.95        28.34         5.46         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 
       12.43        18.25        21.90        18.48        31.27        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 
        6.51         0.10        33.24        14.96         4.93        26.89 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75        13.81        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 
       15.81        13.32        18.74         0.26        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2704 
       56.65        35.24        29.92        21.11        12.23        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 
       92.71        21.93        49.48        66.54        56.91        48.49 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 
       42.64        29.85        23.57        26.83        52.67        70.13 
TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN 
       70.42        55.30        70.62        58.65        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 
       25.28        89.29        16.37        36.16        34.59        16.96 
TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
       43.10         0.99         1.02         2.01         0.92        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         7.07        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 
       25.97        40.01        22.98         4.04        22.98        30.02 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-70-6723 
        4.01         2.73         6.64         6.94        13.35        12.33 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 
       73.12        75.09        23.28        11.18         0.49        73.22 
TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8131 
       70.13         0.16        46.78        32.55        86.76        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       53.92        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       27.39        66.51        54.41        60.53       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
      150.25         5.92        61.94        27.62        40.24         6.41 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
       36.53        34.95        31.30        32.91         1.38        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       18.94        25.15        19.04        24.13        31.56        26.79 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       34.52        10.09         0.76        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        3.09        32.71         2.01         7.76        36.59        38.14 
TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
       12.59        18.08        30.28        34.13        30.97        19.86 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 
       24.36        19.73        16.21        15.85        15.29        29.92 
TCGA-90-6837 TCGA-90-7769 TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       24.92        11.77        10.59         2.70         3.48         4.01 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        4.01         5.03        14.14        17.69        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       27.16        18.15         2.01        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HH 
       20.71        12.89        16.11        13.18        13.41         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HO TCGA-NC-A5HT TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       13.74        43.92        26.43        12.72        43.89         0.20 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.03               0.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            156.66             173.82 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             21.68              21.80 
[1] "0.0 - 156.7 (21.7)" "0.1 - 173.8 (21.8)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         2       20       35        0        18        31
  15Q LOSS WILD-TYPE       0       69      117        2        47        64
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  15Q LOSS MUTATED           2         22          7        3
  15Q LOSS WILD-TYPE         1         41         12        4
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 20                 69
  STAGE IB                 35                117
  STAGE II                  0                  2
  STAGE IIA                18                 47
  STAGE IIB                31                 64
  STAGE III                 2                  1
  STAGE IIIA               22                 41
  STAGE IIIB                7                 12
  STAGE IV                  3                  4
[1] 10  2
[1] 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    25  86  22   8
  15Q LOSS WILD-TYPE  87 208  49  16
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               25                 87
  T2               86                208
  T3               22                 49
  T4                8                 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
  15Q LOSS MUTATED    79  45  15   1
  15Q LOSS WILD-TYPE 238  88  25   4
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               79                238
  N1               45                 88
  N2               15                 25
  N3                1                  4
[1] 4 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   111   3
  15Q LOSS WILD-TYPE 300   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    111    3
  15Q LOSS WILD-TYPE  300    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              111                300
  1                3                  4
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    39 102
  15Q LOSS WILD-TYPE  91 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     39  102
  15Q LOSS WILD-TYPE   91  269
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               39                 91
  MALE                102                269
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   101  18
  15Q LOSS WILD-TYPE 283  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    101   18
  15Q LOSS WILD-TYPE  283   35
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               101                283
  YES               18                 35
[1] 2 2
[1] FALSE
D68V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED                                       2
  15Q LOSS WILD-TYPE                                    13
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  15Q LOSS MUTATED                                        1
  15Q LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED                                         1
  15Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                           137
  15Q LOSS WILD-TYPE                                                         342
D68V10, multiclass
                                                             clus
vv                                                            15Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              137
                                                             clus
vv                                                            15Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                342
[1] 4 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   113   3   2   5
  15Q LOSS WILD-TYPE 286   9   2  18
D68V13, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              113                286
  R1                3                  9
  R2                2                  2
  RX                5                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       4                        13    94
  15Q LOSS WILD-TYPE     5                        18   255
D68V14, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN               13                 18
  WHITE                                   94                255
[1] 3 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     2  86
  15Q LOSS WILD-TYPE   6 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   86
  15Q LOSS WILD-TYPE    6  231
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               86                231
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    94  66
  16P LOSS WILD-TYPE 186 148
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               160                334 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                66                148 
$`16P LOSS MUTATED`
TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-33-4533 TCGA-33-6737 TCGA-34-2609 
        4.80        31.99         6.18       133.74        19.76        31.27 
TCGA-43-7657 TCGA-43-7658 TCGA-56-8201 TCGA-56-A4BY TCGA-63-A5MH TCGA-94-7557 
        7.76        78.18        13.05        17.85        66.61         0.16 
TCGA-96-A4JK TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HR TCGA-NK-A5CT TCGA-O2-A52W 
       19.36         5.69         0.07        40.90        65.65         8.58 
TCGA-18-3415 TCGA-18-5592 TCGA-21-1070 TCGA-21-1076 TCGA-21-1080 TCGA-21-5786 
       92.15        49.94       119.54        60.89       122.43        33.93 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
       21.99         4.31        14.10        48.33        24.13        38.17 
TCGA-22-4604 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-33-AASB 
       13.12        11.77         0.79        71.34        11.74         6.94 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-5236 TCGA-34-5239 
       44.19       118.36        27.16         2.63         9.07        60.30 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8455 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 
       44.75        39.32         4.04       133.25       126.58        68.58 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5040 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 
      102.18         1.71        17.06        39.12        27.91        22.98 
TCGA-43-7656 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-6025 TCGA-52-7622 
       19.59        11.77        14.20        13.32        10.65        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-56-7580 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
        5.46        30.35        30.41        17.49        33.24        14.96 
TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-58-8391 TCGA-58-8392 
        1.35        15.81        20.94        13.32        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2695 TCGA-60-2708 
       34.78        85.12        34.36        56.65        21.11        80.45 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 
       50.33        42.64         3.19        35.90        23.57        52.67 
TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MY TCGA-66-2727 
      102.67        58.65        45.57        25.28        34.59        16.96 
TCGA-66-2734 TCGA-66-2753 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 
       43.10         1.02        43.99        21.01         0.99         7.07 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 
        3.98        12.00         1.97        25.97        40.01        22.98 
TCGA-66-2792 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-77-6842 TCGA-77-7139 
       30.02        49.05         6.64        13.35        29.56       140.09 
TCGA-77-7142 TCGA-77-7463 TCGA-77-8130 TCGA-77-8136 TCGA-77-8140 TCGA-77-8143 
       73.22        46.78       156.66        39.09        11.54        26.40 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 
       60.53        36.36         5.92        27.62        38.86         6.41 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 
       34.95        31.30        32.91        18.94        24.13        31.56 
TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8580 
       10.09        16.77         5.29         3.09         2.01        36.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A53L 
       18.08        22.59        34.13        19.86        19.73        12.39 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-92-8064 TCGA-94-8035 TCGA-96-7544 
        3.65         2.93        22.62         5.26         4.01        71.01 
TCGA-96-8169 TCGA-98-A53A TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW 
       18.31        18.15        18.58        12.89        16.11        13.41 
TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HT 
       64.54        13.74         4.21         2.89        49.28        26.43 
TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A5IB TCGA-XC-AA0X 
       83.57        33.07        11.18         0.20 

$`16P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20         4.47       123.19        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 
       48.82        60.66        64.93        22.06       129.01         1.55 
TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-8118 
       31.50        28.96        17.88        22.49        18.38         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       11.61        12.03        19.99         3.45        17.00        16.77 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       21.04         0.13         3.58        41.42         9.01        35.34 
TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 
       32.32         8.02        20.78        42.08        30.81         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-8020 
       14.07        21.04        18.38        16.14        57.07         2.76 
TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5D1 TCGA-NK-A7XE 
       21.21        19.10        76.80        39.85        16.80         0.43 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 
       75.75       117.57        11.34        23.54        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
       86.96         2.79       154.32        46.88        99.16        70.16 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       34.78        15.58        31.73         9.34       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0944 TCGA-22-1005 
       31.63        88.11        41.69        10.82         7.33        64.21 
TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 
        1.74        27.02        20.48        35.08         0.56        34.75 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       32.02        19.30         9.57        63.55        14.63        44.25 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       86.30        79.20        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       16.64        97.94        79.53       173.82       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       14.07        54.44        63.35         4.70         0.30        36.62 
TCGA-33-AASD TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
      110.99        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 
       50.66        16.93         4.96         1.12        38.79        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       33.90         4.01         0.43         0.39         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        7.46         7.82         6.81         0.39         3.39        37.58 
TCGA-37-A5EN TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
       21.70       111.35        55.20        82.52        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
       60.53        36.39        68.38        71.18        55.56        40.21 
TCGA-43-2581 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       38.66        33.11        24.89        21.47         5.46         3.81 
TCGA-43-8115 TCGA-43-A475 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       13.38         9.73        12.16        13.02         9.83         4.44 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7811 TCGA-52-7812 
       13.91         0.39         0.39        29.95         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 
       28.96        12.43        18.25        21.90        18.48        14.53 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8083 TCGA-56-8304 
       31.27        19.76         6.51         0.10         4.93         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       26.89        14.07         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
        9.93        20.25        19.23        18.74         0.26        14.47 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46M TCGA-58-A46N 
        0.03        13.25        13.55        29.95        35.24        29.92 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       12.23        10.22        96.82        37.94        92.71        21.93 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2722 TCGA-60-2725 
       49.48        66.54        56.91        48.49        29.85        26.83 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG 
       11.77        70.13        70.42        68.15        55.30        70.62 
TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       59.97        14.99        11.34        89.29        78.28        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
       36.16        53.88         2.01        21.07         0.99         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
        0.92         0.99        25.05         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2783 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 
       12.03        24.95        22.98         4.04         5.03        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J 
       54.08         4.01         2.73         6.94        16.18        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.07        12.33        73.12        75.09        23.28        11.18 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8007 
        0.49        70.13       106.95         0.16        32.55         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
       86.76        55.73        37.81        12.59        53.92        17.72 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
      104.09        27.39         6.97        66.51        54.41        65.49 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6175 
      126.18       132.36       150.25        22.29        61.94         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       41.39        40.24        36.53         1.38         1.15        29.95 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
       25.15        19.04        26.79        30.64        34.52         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 
       13.22        22.45        32.71        15.39         7.76        38.14 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       12.59        30.28        30.97        24.36        30.48        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 
       16.21        15.85        14.96        15.29        29.92        24.92 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       11.77        20.22        10.59         2.70         3.48         4.01 
TCGA-92-8065 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8170 
        2.30         5.03        26.63        14.14        17.69        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       27.68        21.44        30.81        30.67        21.34        27.16 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-LA-A446 TCGA-MF-A522 
        2.01        27.02        20.32        20.71        13.18        11.84 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.54         1.22        57.30        43.92        25.32        14.73 
TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
        3.65         3.72        12.72        43.89 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            156.66             173.82 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            22.980             21.275 
[1] "0.1 - 156.7 (23.0)" "0.0 - 173.8 (21.3)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         2       26       49        0        19        39
  16P LOSS WILD-TYPE       0       63      103        2        46        56
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  16P LOSS MUTATED           1         23          2        1
  16P LOSS WILD-TYPE         2         40         17        6
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 26                 63
  STAGE IB                 49                103
  STAGE II                  0                  2
  STAGE IIA                19                 46
  STAGE IIB                39                 56
  STAGE III                 1                  2
  STAGE IIIA               23                 40
  STAGE IIIB                2                 17
  STAGE IV                  1                  6
[1] 10  2
[1] 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    29 101  26   7
  16P LOSS WILD-TYPE  83 193  45  17
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               29                 83
  T2              101                193
  T3               26                 45
  T4                7                 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
  16P LOSS MUTATED   107  45  11   0
  16P LOSS WILD-TYPE 210  88  29   5
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0              107                210
  N1               45                 88
  N2               11                 29
  N3                0                  5
[1] 4 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   136   1
  16P LOSS WILD-TYPE 275   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    136    1
  16P LOSS WILD-TYPE  275    6
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0              136                275
  1                1                  6
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    47 116
  16P LOSS WILD-TYPE  83 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     47  116
  16P LOSS WILD-TYPE   83  255
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               47                 83
  MALE                116                255
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   133  16
  16P LOSS WILD-TYPE 251  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    133   16
  16P LOSS WILD-TYPE  251   37
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO               133                251
  YES               16                 37
[1] 2 2
[1] FALSE
D69V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED                                       8
  16P LOSS WILD-TYPE                                     7
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  16P LOSS MUTATED                                        0
  16P LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED                                         0
  16P LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                           155
  16P LOSS WILD-TYPE                                                         324
D69V10, multiclass
                                                             clus
vv                                                            16P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              155
                                                             clus
vv                                                            16P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D69V11, continuous
D69V12, continuous
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED   133   1   0   6
  16P LOSS WILD-TYPE 266  11   4  17
D69V13, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0              133                266
  R1                1                 11
  R2                0                  4
  RX                6                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                        15   107
  16P LOSS WILD-TYPE     8                        16   242
D69V14, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN               15                 16
  WHITE                                  107                242
[1] 3 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     2 100
  16P LOSS WILD-TYPE   6 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2  100
  16P LOSS WILD-TYPE    6  217
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO              100                217
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   108  73
  16Q LOSS WILD-TYPE 172 141
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               181                313 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                73                141 
$`16Q LOSS MUTATED`
TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 
        4.80        31.99         6.18       133.74        19.76        31.50 
TCGA-34-2609 TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-56-7221 TCGA-56-8201 
       31.27        22.49         7.76        78.18        19.99        13.05 
TCGA-56-A4BY TCGA-60-2711 TCGA-63-A5MH TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK 
       17.85        41.42        66.61         0.16        16.14        19.36 
TCGA-98-A539 TCGA-NC-A5HR TCGA-NK-A5CT TCGA-O2-A52W TCGA-18-3415 TCGA-18-3419 
        5.69        40.90        65.65         8.58        92.15        92.42 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-22-0940 
       49.94       119.54        60.89       122.43        43.23        21.99 
TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 
        4.31        14.10        48.33        24.13        38.17        13.12 
TCGA-22-5473 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 
       63.55         0.79        71.34        79.20        11.74        62.86 
TCGA-33-4586 TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-5231 
       14.07        44.19       118.36        27.16         2.63        65.23 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8455 
        9.07        60.30        44.75        39.32         4.96         4.04 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
      133.25       126.58       111.35       102.18         1.71         1.94 
TCGA-39-5040 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-8116 TCGA-43-A56U 
       17.06        39.12        33.11        27.91        11.77        14.20 
TCGA-46-3765 TCGA-46-6025 TCGA-46-6026 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
       13.32        10.65        13.91        28.34         5.46        30.35 
TCGA-56-7222 TCGA-56-7580 TCGA-56-7730 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       18.48        30.41         6.51        17.49        33.24        14.96 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BX 
       26.89        14.07         1.35         9.93        20.94        13.32 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.25        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2710 TCGA-60-2713 
       85.12        56.65        35.24        21.11        66.54        56.91 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-63-6202 TCGA-63-7023 
       50.33        42.64         3.19        35.90        52.67        55.30 
TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MY TCGA-66-2727 
      102.67        58.65        45.57        25.28        34.59        16.96 
TCGA-66-2734 TCGA-66-2753 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
       43.10         1.02         0.92        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2778 TCGA-66-2782 
        0.99         2.01         7.07        23.01        19.00        12.00 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 
       40.01         4.04        22.98        30.02        10.06        49.05 
TCGA-68-7756 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-7139 TCGA-77-7142 
        6.64        13.35        14.73        29.56       140.09        73.22 
TCGA-77-7463 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8150 
       46.78        39.09       104.09        11.54        26.40        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 
       65.49        36.36        38.86        40.24         6.41        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7950 TCGA-85-8071 TCGA-85-8353 TCGA-85-8355 
       31.30        32.91        18.94        26.79         3.09         2.01 
TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
       36.59        18.08        22.59        34.13        30.97        19.86 
TCGA-85-A4QR TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE 
       19.73        15.29         3.65         2.93        20.22        22.62 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-A4VJ TCGA-96-8169 TCGA-98-A538 
        5.26         2.30         4.01        14.14        18.31        27.16 
TCGA-98-A53A TCGA-98-A53I TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN 
       18.15        18.58        64.54        13.74         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A5IB 
       43.92        14.73        26.43        83.57        33.07        11.18 
TCGA-XC-AA0X 
        0.20 

$`16Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20         4.47       123.19        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 
       48.82        60.66        64.93        22.06       129.01         1.55 
TCGA-34-2605 TCGA-39-5039 TCGA-43-5668 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       28.96        17.88        18.38         2.93        11.61        12.03 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
        3.45        17.00        16.77        21.04         0.13         3.58 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
        9.01        35.34        32.32         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 
       30.81         9.50        14.07        21.04        18.38        57.07 
TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        2.76        21.21        19.10         0.07        76.80        39.85 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       16.80         0.43        75.75       117.57        11.34        23.54 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1071 TCGA-21-1072 
       36.07        86.96         2.79       154.32        46.88        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
       70.16        34.78        15.58        31.73         9.34       119.80 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
       31.63        88.11        41.69        33.93        10.82         7.33 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 
       64.21         1.74        27.02        20.48        35.08         0.56 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 
       34.75        32.02        19.30         9.57        11.77        14.63 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
       44.25        86.30        18.84        30.12        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 
       97.94        79.53       173.82       103.53       151.27        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       63.35         4.70         0.30        36.62         6.94       110.99 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 
       61.61        32.88        81.24        74.66        50.66        16.93 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        1.12        38.79        26.43        33.90         4.01         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.39         7.96         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5021 TCGA-39-5022 
        0.39         3.39        37.58        21.70        68.58        55.20 
TCGA-39-5024 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       82.52        24.33        60.53        36.39        68.38        71.18 
TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       55.56        40.21        38.66        22.98        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-A475 TCGA-46-3766 
        5.46         3.81        19.59        13.38         9.73        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       13.02         9.83         4.44         0.39         0.39        29.95 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        8.75        27.45        28.96        12.43        18.25        21.90 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-8083 TCGA-56-8304 
       14.53        31.27        19.76         0.10         4.93         3.48 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
        1.81        22.75        13.81        10.36        20.25        15.81 
TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-A46K 
       19.23        18.74         0.26        14.47         0.03        34.36 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       29.92        12.23        10.22        96.82        37.94        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2716 TCGA-60-2722 TCGA-60-2724 
       21.93        80.45        49.48        48.49        29.85        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MG 
       26.83        11.77        70.13        70.42        68.15        70.62 
TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       59.97        14.99        11.34        89.29        78.28        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
       36.16        53.88         2.01        21.07         0.99         2.01 
TCGA-66-2756 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 
        0.99         2.01         1.02         2.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
        2.01        12.03         3.98        24.95         1.97        25.97 
TCGA-66-2788 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 
       22.98         5.03        54.08         4.01         2.73         6.94 
TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       16.18        12.07        12.33        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 
       11.18         0.49        70.13       106.95         0.16        32.55 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        6.51        86.76        55.73        37.81       156.66        12.59 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 
       53.92        17.72        27.39         6.97        66.51        60.53 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       150.25        22.29         5.92        61.94 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7710 TCGA-85-7843 
       27.62         9.67        41.39        36.53         1.38         1.15 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
       29.95        25.15        19.04        24.13        31.56        30.64 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       34.52        10.09         0.76        13.22        22.45        16.77 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 
        5.29        32.71        15.39         7.76        38.14        12.59 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       30.28        24.36        30.48        27.16        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 TCGA-90-A59Q 
       14.96        29.92        12.39        24.92        11.77        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 
        2.70         3.48         4.01         5.03        26.63        17.69 
TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       71.01        17.46        27.68        21.44        30.81        30.67 
TCGA-98-8023 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 
       21.34         2.01        27.02        20.32        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH 
       16.11        13.18        13.41        11.84         4.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HP TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S 
       57.30         4.21        25.32         3.65         3.72        12.72 
TCGA-O2-A52V 
       43.89 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.16               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            140.09             173.82 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             25.05              21.04 
[1] "0.2 - 140.1 (25.1)" "0.0 - 173.8 (21.0)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         2       28       56        0        23        40
  16Q LOSS WILD-TYPE       0       61       96        2        42        55
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  16Q LOSS MUTATED           1         25          6        1
  16Q LOSS WILD-TYPE         2         38         13        6
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 28                 61
  STAGE IB                 56                 96
  STAGE II                  0                  2
  STAGE IIA                23                 42
  STAGE IIB                40                 55
  STAGE III                 1                  2
  STAGE IIIA               25                 38
  STAGE IIIB                6                 13
  STAGE IV                  1                  6
[1] 10  2
[1] 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    36 112  28   8
  16Q LOSS WILD-TYPE  76 182  43  16
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               36                 76
  T2              112                182
  T3               28                 43
  T4                8                 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
  16Q LOSS MUTATED   118  48  14   3
  16Q LOSS WILD-TYPE 199  85  26   2
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0              118                199
  N1               48                 85
  N2               14                 26
  N3                3                  2
[1] 4 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   156   1
  16Q LOSS WILD-TYPE 255   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    156    1
  16Q LOSS WILD-TYPE  255    6
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              156                255
  1                1                  6
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    56 128
  16Q LOSS WILD-TYPE  74 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     56  128
  16Q LOSS WILD-TYPE   74  243
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               56                 74
  MALE                128                243
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   144  22
  16Q LOSS WILD-TYPE 240  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    144   22
  16Q LOSS WILD-TYPE  240   31
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               144                240
  YES               22                 31
[1] 2 2
[1] FALSE
D70V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED                                       7
  16Q LOSS WILD-TYPE                                     8
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  16Q LOSS MUTATED                                        0
  16Q LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED                                         0
  16Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                           177
  16Q LOSS WILD-TYPE                                                         302
D70V10, multiclass
                                                             clus
vv                                                            16Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              177
                                                             clus
vv                                                            16Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                302
[1] 4 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   144   2   2   7
  16Q LOSS WILD-TYPE 255  10   2  16
D70V13, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0              144                255
  R1                2                 10
  R2                2                  2
  RX                7                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                        13   125
  16Q LOSS WILD-TYPE     8                        18   224
D70V14, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN               13                 18
  WHITE                                  125                224
[1] 3 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     2 113
  16Q LOSS WILD-TYPE   6 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2  113
  16Q LOSS WILD-TYPE    6  204
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO              113                204
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   167 124
  17P LOSS WILD-TYPE 113  90
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               291                203 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               124                 90 
$`17P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-21-A5DI TCGA-22-1000 
       12.20         4.47         4.80        31.99        32.19        14.93 
TCGA-22-5472 TCGA-22-A5C4 TCGA-34-2604 TCGA-43-5668 TCGA-43-7658 TCGA-43-A474 
       64.93        22.06        31.50        18.38        78.18        11.61 
TCGA-43-A56V TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       12.03        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
        9.01        32.32        66.61        30.81         9.50        14.07 
TCGA-94-7033 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HM 
       21.04        16.14        57.07         5.69         0.07        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
       40.90        65.65        16.80       117.57        23.54        92.15 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 TCGA-21-1075 TCGA-21-1077 
       92.42        86.96       154.32       119.54        70.16        34.78 
TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 
      122.43       119.80        43.23        31.63        88.11        33.93 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       10.82         7.33         4.31         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
       20.48        48.33        24.13         0.56        38.17        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
       32.02        19.30         9.57        63.55        44.25         0.79 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       71.34        79.20        18.84        62.86        56.32        16.64 
TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A5GW 
       79.53       151.27        14.07        54.44        63.35         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
       36.62         6.94        27.16        61.61        32.88        65.23 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       38.79         4.04        26.43        33.90         4.01         0.43 
TCGA-37-3792 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        0.39         7.82         6.81         0.39         3.39        37.58 
TCGA-37-A5EN TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 
       21.70       126.58        82.52       102.18        24.33         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       36.39        68.38        17.06        40.21        38.66        39.12 
TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
       27.91        22.98        19.59        13.38        11.77         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-52-7622 
       14.20        13.32        10.65        13.91         0.39        28.34 
TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 
       30.35        27.45        28.96        12.43        18.25        14.53 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7822 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       31.27        30.41        17.49         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       14.07         1.35         1.81        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A62T TCGA-58-8386 
       20.25        15.81        20.94        13.32        14.47         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M 
       13.25        13.55        29.95        34.78        56.65        35.24 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       21.11        10.22        96.82        92.71        21.93        80.45 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       66.54        56.91        50.33        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 
       35.90        26.83        52.67        70.13        70.42        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MT TCGA-63-A5MV 
      102.67        70.62        58.65        59.97        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2753 
       53.88        34.59        16.96        43.10        21.07         1.02 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 
        2.01        43.99        25.05         0.99         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 
        2.01         7.07        19.00         3.02         2.01        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 
        3.98        12.00        24.95         1.97        25.97        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-68-7757 TCGA-77-6842 
        4.04         5.03        10.06         4.01         6.94        29.56 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       75.09        23.28       140.09         0.49        70.13       106.95 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        0.16        32.55        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       12.59        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G1 
       27.39         6.97        66.51        54.41        60.53       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 
      150.25        22.29         5.92        61.94        38.86        41.39 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 
       36.53        34.95         1.38        29.95        24.13        31.56 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8479 TCGA-85-8584 TCGA-85-8666 
       34.52         0.76        13.22        15.39        12.59        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
       30.28        34.13        30.97        19.86        30.48        19.73 
TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED 
       16.21        15.29        29.92        12.39         2.93        20.22 
TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8490 TCGA-94-8491 
       10.59         3.48         4.01         2.30         5.03        26.63 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 
       17.69        71.01        17.46        27.68        30.81        30.67 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J TCGA-L3-A4E7 TCGA-NC-A5HF 
       27.16        18.15         2.01        20.71        12.89         4.54 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       64.54        57.30         4.21        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       14.73        83.57         3.65        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

$`17P LOSS WILD-TYPE`
TCGA-18-3409 TCGA-18-4083 TCGA-18-5595 TCGA-22-1017 TCGA-22-5471 TCGA-33-4532 
      123.19         6.18        27.19        48.82        60.66       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 
      133.74         1.55        19.76        28.96        31.27        17.88 
TCGA-43-2578 TCGA-43-7657 TCGA-43-8118 TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
       22.49         7.76         2.93        19.99        13.05         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-60-2715 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
       17.00        16.77        35.34         8.02        20.78        42.08 
TCGA-94-7557 TCGA-94-7943 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH 
        0.16        18.38        19.36         2.76        21.21        19.10 
TCGA-NC-A5HE TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3412 TCGA-18-3417 
       76.80         0.43         8.58        75.75        11.34        36.07 
TCGA-18-4086 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 
        2.79        49.94        46.88        99.16        60.89        15.58 
TCGA-21-1079 TCGA-21-1081 TCGA-21-5784 TCGA-22-0940 TCGA-22-1005 TCGA-22-4593 
       31.73         9.34        41.69        21.99        64.21        35.08 
TCGA-22-4601 TCGA-22-4613 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 
       34.75        11.77        14.63        86.30        11.74        30.12 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-A4WN TCGA-33-AASD TCGA-33-AASI 
       97.94       173.82       103.53         4.70       110.99        44.19 
TCGA-33-AASJ TCGA-34-2596 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
      118.36         2.63        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       50.66        16.93        44.75        39.32         4.96         1.12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
        7.96         8.12         7.46       133.25       111.35        68.58 
TCGA-39-5022 TCGA-39-5028 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-3920 
       55.20         1.71        60.53        71.18        55.56        33.11 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-46-3766 TCGA-46-3767 
       24.89        21.47         5.46         3.81        12.16        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 
        9.83         4.44         0.39        29.95         5.46         8.75 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 
       21.90        18.48        19.76         6.51         0.10        33.24 
TCGA-56-8082 TCGA-56-8623 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8391 
       14.96        22.75        19.23        18.74         0.26        71.24 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N TCGA-60-2697 TCGA-60-2704 
       16.47        85.12        34.36        29.92        12.23        37.94 
TCGA-60-2709 TCGA-60-2716 TCGA-60-2724 TCGA-60-2726 TCGA-63-7022 TCGA-63-A5ML 
       49.48        48.49        23.57        11.77        68.15        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-66-2737 
       14.99        11.34        25.28        89.29        78.28         2.01 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2765 TCGA-66-2770 
        0.99         0.92         0.99        21.01         2.01        23.01 
TCGA-66-2778 TCGA-66-2787 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 
       19.00        40.01        22.98        30.02        54.08        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        2.73         6.64        13.35        16.18        14.73        12.07 
TCGA-70-6723 TCGA-77-6843 TCGA-77-7138 TCGA-77-7142 TCGA-77-7463 TCGA-77-8007 
       12.33        73.12        11.18        73.22        46.78         6.51 
TCGA-77-8143 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5GF TCGA-85-6175 
       26.40        65.49        36.36       126.18        27.62         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 
       40.24         6.41        31.30        32.91         1.15        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8350 
       25.15        19.04        26.79        30.64        10.09        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
       16.77         5.29         3.09        32.71         2.01         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A510 
       36.59        38.14        18.08        24.36        27.16        15.85 
TCGA-85-A511 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 
       14.96         3.65        24.92        11.77        22.62         2.70 
TCGA-92-8064 TCGA-94-8035 TCGA-94-A4VJ TCGA-96-8169 TCGA-98-7454 TCGA-98-8023 
        5.26         4.01        14.14        18.31        21.44        21.34 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       27.02        20.32        18.58        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HT 
       11.84         1.22        13.74         2.89        26.43 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            156.66             173.82 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             23.54              19.99 
[1] "0.0 - 156.7 (23.5)" "0.1 - 173.8 (20.0)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         1       53       83        1        39        54
  17P LOSS WILD-TYPE       1       36       69        1        26        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  17P LOSS MUTATED           3         39         12        5
  17P LOSS WILD-TYPE         0         24          7        2
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 53                 36
  STAGE IB                 83                 69
  STAGE II                  1                  1
  STAGE IIA                39                 26
  STAGE IIB                54                 41
  STAGE III                 3                  0
  STAGE IIIA               39                 24
  STAGE IIIB               12                  7
  STAGE IV                  5                  2
[1] 10  2
[1] 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    69 166  45  12
  17P LOSS WILD-TYPE  43 128  26  12
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               69                 43
  T2              166                128
  T3               45                 26
  T4               12                 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   181  72  31   4
  17P LOSS WILD-TYPE 136  61   9   1
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              181                136
  N1               72                 61
  N2               31                  9
  N3                4                  1
[1] 4 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   239   5
  17P LOSS WILD-TYPE 172   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    239    5
  17P LOSS WILD-TYPE  172    2
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              239                172
  1                5                  2
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    74 218
  17P LOSS WILD-TYPE  56 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     74  218
  17P LOSS WILD-TYPE   56  153
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               74                 56
  MALE                218                153
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   219  29
  17P LOSS WILD-TYPE 165  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    219   29
  17P LOSS WILD-TYPE  165   24
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               219                165
  YES               29                 24
[1] 2 2
[1] FALSE
D71V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                       9
  17P LOSS WILD-TYPE                                     6
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  17P LOSS MUTATED                                        2
  17P LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                         1
  17P LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                           280
  17P LOSS WILD-TYPE                                                         199
D71V10, multiclass
                                                             clus
vv                                                            17P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              280
                                                             clus
vv                                                            17P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
D71V12, continuous
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   241   6   2  10
  17P LOSS WILD-TYPE 158   6   2  13
D71V13, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              241                158
  R1                6                  6
  R2                2                  2
  RX               10                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       6                        14   198
  17P LOSS WILD-TYPE     3                        17   151
D71V14, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    6                  3
  BLACK OR AFRICAN AMERICAN               14                 17
  WHITE                                  198                151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V15, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4 176
  17P LOSS WILD-TYPE   4 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  176
  17P LOSS WILD-TYPE    4  141
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              176                141
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    59  32
  17Q LOSS WILD-TYPE 221 182
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                91                403 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                32                182 
$`17Q LOSS MUTATED`
TCGA-21-A5DI TCGA-22-5472 TCGA-43-A56V TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 
       32.19        64.93        12.03        21.04         3.58        41.42 
TCGA-77-A5GB TCGA-94-7557 TCGA-NK-A5CT TCGA-18-3414 TCGA-21-1070 TCGA-22-1011 
       30.81         0.16        65.65        23.54       119.54         1.74 
TCGA-22-1016 TCGA-22-4595 TCGA-22-4596 TCGA-22-4605 TCGA-22-5478 TCGA-33-4583 
       27.02        24.13         0.56        32.02         0.79       151.27 
TCGA-33-4587 TCGA-34-2600 TCGA-34-5241 TCGA-34-8455 TCGA-34-A5IX TCGA-37-4141 
       54.44        61.61        16.93         4.04        33.90         0.39 
TCGA-39-5029 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 
       24.33        68.38        17.06        38.66        39.12        27.91 
TCGA-43-7656 TCGA-43-A56U TCGA-52-7622 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 
       19.59        14.20        28.34        30.35        12.43        18.25 
TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 TCGA-56-8628 TCGA-56-A62T 
       30.41        17.49         1.35        13.81        20.25        14.47 
TCGA-58-8393 TCGA-58-A46M TCGA-60-2695 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 
       34.78        35.24        21.11        80.45        50.33        42.64 
TCGA-60-2720 TCGA-60-2723 TCGA-63-7020 TCGA-63-A5MG TCGA-63-A5MI TCGA-66-2769 
        3.19        35.90        70.13        70.62        58.65         7.07 
TCGA-66-2771 TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 TCGA-77-8008 TCGA-77-8130 
       19.00        12.03        12.00        25.97        86.76       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8150 
       12.59        53.92        17.72       104.09        27.39        54.41 
TCGA-77-A5G1 TCGA-77-A5GH TCGA-85-7696 TCGA-85-7697 TCGA-85-7950 TCGA-85-8479 
      132.36        38.86        36.53        34.95        18.94        15.39 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A513 
       34.13        30.97        19.86        30.48        16.21        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-92-8063 TCGA-92-8065 TCGA-94-8491 TCGA-94-A5I6 
       12.39         3.65         4.01         2.30        26.63        17.69 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-A538 TCGA-L3-A4E7 TCGA-NC-A5HF TCGA-NC-A5HQ 
       27.68        30.81        27.16        12.89         4.54        14.73 
TCGA-NK-A5CX 
        3.65 

$`17Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 
       27.19        14.93        48.82        60.66        22.06       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      133.74         1.55        19.76        31.50        28.96        31.27 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       17.88        22.49        18.38         7.76        78.18         2.93 
TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       11.61        19.99        13.05         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
       17.85         0.13         9.01        35.34        32.32        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
        8.02        20.78        42.08         9.50        14.07        21.04 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
       18.38        16.14        57.07        19.36         2.76         5.69 
TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
       21.21        19.10         0.07        76.80        39.85        40.90 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 
       16.80         0.43         8.58        75.75       117.57        11.34 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       92.15        36.07        92.42        86.96         2.79       154.32 
TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
       49.94        46.88        99.16        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       15.58        31.73       122.43         9.34       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
       31.63        88.11        41.69        33.93        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
        7.33         4.31        64.21        14.10        20.48        35.08 
TCGA-22-4594 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 
       48.33        38.17        34.75        13.12        19.30         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
       11.77        63.55        14.63        44.25        86.30        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
       16.64        97.94        79.53       173.82       103.53        14.07 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       63.35         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 
       44.19       118.36        27.16         2.63        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
       81.24        74.66         9.07        60.30        50.66        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 
       39.32         4.96         1.12        38.79        26.43         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         7.96         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 
        6.81         3.39        37.58        21.70       133.25       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      111.35        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
        1.94        60.53        36.39        71.18        55.56        40.21 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       33.11        22.98        24.89        21.47         5.46         3.81 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       13.38        11.77         9.73        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
        9.83         4.44        10.65        13.91         0.39         0.39 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 
       29.95         5.46         8.75        27.45        28.96        21.90 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       18.48        14.53        31.27        19.76         6.51         0.10 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       33.24        14.96         4.93         3.48        26.89        14.07 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D 
        1.81        22.75        10.36         9.93        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 
       19.23        13.32        18.74         0.26         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K 
       13.55        29.95        71.24        16.47        85.12        34.36 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       56.65        29.92        12.23        10.22        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 
       92.71        21.93        49.48        66.54        56.91        48.49 
TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 
       29.85        23.57        26.83        11.77        52.67        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
       68.15        55.30       102.67        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       11.34        25.28        89.29        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       53.88        34.59        16.96        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        0.99         1.02         2.01         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 
        2.01        23.01         3.02         2.01        19.00         3.98 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       24.95         1.97        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         6.94        13.35        16.18        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       11.18       140.09         0.49        73.22        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 
        0.16        46.78        32.55         6.51        55.73        37.81 
TCGA-77-8136 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
       39.09        11.54        26.40         6.97        66.51        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       60.53        36.36       126.18       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
       61.94        27.62         9.67        41.39        40.24         6.41 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 
       31.30        32.91         1.38         1.15        29.95        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       19.04        24.13        31.56        26.79        30.64        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       10.09         0.76        13.22        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        3.09        32.71         2.01         7.76        36.59        38.14 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR 
       12.59        18.08        22.59        30.28        24.36        19.73 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-90-6837 TCGA-90-7767 
       27.16        15.85        14.96        15.29        24.92         2.93 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       11.77        20.22        22.62        10.59         2.70         3.48 
TCGA-92-8064 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        5.26         4.01         5.03        14.14        71.01        18.31 
TCGA-96-8170 TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B 
       17.46        21.44        30.67        21.34        18.15         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 
       27.02        20.32        18.58        20.71        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       13.41        11.84        64.54         1.22        57.30        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT 
        4.21         2.89        49.28        43.92        25.32        26.43 
TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       83.57        33.07         3.72        12.72        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.16               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            156.66             173.82 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             26.63              21.21 
[1] "0.2 - 156.7 (26.6)" "0.0 - 173.8 (21.2)"
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0       20       28        0        10        18
  17Q LOSS WILD-TYPE       2       69      124        2        55        77
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  17Q LOSS MUTATED           0         11          2        2
  17Q LOSS WILD-TYPE         3         52         17        5
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 20                 69
  STAGE IB                 28                124
  STAGE II                  0                  2
  STAGE IIA                10                 55
  STAGE IIB                18                 77
  STAGE III                 0                  3
  STAGE IIIA               11                 52
  STAGE IIIB                2                 17
  STAGE IV                  2                  5
[1] 10  2
[1] 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    24  46  17   4
  17Q LOSS WILD-TYPE  88 248  54  20
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               24                 88
  T2               46                248
  T3               17                 54
  T4                4                 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                  N0  N1  N2  N3
  17Q LOSS MUTATED    67  14   7   0
  17Q LOSS WILD-TYPE 250 119  33   5
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               67                250
  N1               14                119
  N2                7                 33
  N3                0                  5
[1] 4 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    77   2
  17Q LOSS WILD-TYPE 334   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     77    2
  17Q LOSS WILD-TYPE  334    5
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               77                334
  1                2                  5
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    28  63
  17Q LOSS WILD-TYPE 102 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     28   63
  17Q LOSS WILD-TYPE  102  308
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               28                102
  MALE                 63                308
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    75   8
  17Q LOSS WILD-TYPE 309  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     75    8
  17Q LOSS WILD-TYPE  309   45
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                75                309
  YES                8                 45
[1] 2 2
[1] FALSE
D72V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                       1
  17Q LOSS WILD-TYPE                                    14
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  17Q LOSS MUTATED                                        1
  17Q LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                         1
  17Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                            88
  17Q LOSS WILD-TYPE                                                         391
D72V10, multiclass
                                                             clus
vv                                                            17Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               88
                                                             clus
vv                                                            17Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                391
[1] 4 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    73   2   0   5
  17Q LOSS WILD-TYPE 326  10   4  18
D72V13, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               73                326
  R1                2                 10
  R2                0                  4
  RX                5                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       4                         7    59
  17Q LOSS WILD-TYPE     5                        24   290
D72V14, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                7                 24
  WHITE                                   59                290
[1] 3 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  63
  17Q LOSS WILD-TYPE   6 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   63
  17Q LOSS WILD-TYPE    6  254
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               63                254
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    83  58
  18P LOSS WILD-TYPE 197 156
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               141                353 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                58                156 
$`18P LOSS MUTATED`
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 
       32.19        14.93        48.82       133.74         1.55        19.76 
TCGA-34-2609 TCGA-56-7221 TCGA-56-8305 TCGA-63-A5MH TCGA-68-8250 TCGA-90-7766 
       31.27        19.99         3.45        66.61         8.02         9.50 
TCGA-94-7557 TCGA-94-7943 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD 
        0.16        18.38        19.36         2.76         5.69         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3414 
       76.80        39.85        40.90        65.65        16.80        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 TCGA-21-1071 TCGA-21-1080 
       92.15        36.07        86.96       119.54        46.88       122.43 
TCGA-21-5787 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4594 TCGA-22-4601 
       10.82        14.10        27.02        35.08        48.33        34.75 
TCGA-22-4613 TCGA-22-5478 TCGA-22-5482 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       11.77         0.79        11.74        97.94        79.53       103.53 
TCGA-33-6738 TCGA-33-A5GW TCGA-34-2608 TCGA-34-5241 TCGA-34-7107 TCGA-34-8455 
       63.35         0.30        32.88        16.93         1.12         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-39-5011 
       26.43        33.90         8.12         7.46         7.82       133.25 
TCGA-39-5028 TCGA-39-5036 TCGA-43-3394 TCGA-43-6143 TCGA-43-6647 TCGA-43-7656 
        1.71        71.18        39.12        22.98        24.89        19.59 
TCGA-43-8115 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-52-7810 TCGA-56-1622 
       13.38         9.83        10.65         0.39        30.35        28.96 
TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-8307 TCGA-56-8503 TCGA-56-8624 
       12.43        21.90        18.48        26.89         1.35        13.81 
TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T TCGA-58-A46K 
        9.93        15.81        19.23        18.74        14.47        34.36 
TCGA-58-A46M TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2720 TCGA-63-A5MB 
       35.24        92.71        21.93        80.45         3.19       102.67 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2744 
       25.28        89.29        78.28        16.37        34.59         0.99 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2766 TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 
        1.02         0.92         1.02         3.02        12.03         3.98 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7757 
        1.97        25.97         5.03        30.02         4.01         6.94 
TCGA-77-6842 TCGA-77-8007 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 
       29.56         6.51        12.59        39.09       104.09        11.54 
TCGA-77-8144 TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 
       27.39       132.36         5.92        61.94        38.86         9.67 
TCGA-85-6560 TCGA-85-7697 TCGA-85-7950 TCGA-85-8287 TCGA-85-8355 TCGA-85-8481 
       41.39        34.95        18.94         0.76         2.01         7.76 
TCGA-85-8584 TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A511 TCGA-85-A53L TCGA-90-7767 
       12.59        19.86        19.73        14.96        12.39         2.93 
TCGA-90-A4ED TCGA-92-7341 TCGA-94-A5I6 TCGA-96-8170 TCGA-98-8023 TCGA-98-A538 
       20.22         3.48        17.69        17.46        21.34        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HO 
       18.15         2.01        20.71        11.84        64.54        43.92 
TCGA-NC-A5HP TCGA-O2-A52Q TCGA-O2-A52S 
       25.32         3.72        12.72 

$`18P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-34-2604 
       27.19        60.66        64.93        22.06       129.01        31.50 
TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       28.96        17.88        22.49        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 
        2.93        11.61        12.03        13.05        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
       17.85        21.04         0.13         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 
       35.34        32.32        20.78        42.08        30.81        14.07 
TCGA-94-7033 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-A53D TCGA-J1-A4AH TCGA-NK-A7XE 
       21.04        16.14        57.07        21.21        19.10         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3419 TCGA-18-4086 
        8.58        75.75       117.57        11.34        92.42         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      154.32        49.94        99.16        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       15.58        31.73         9.34       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       88.11        41.69        33.93        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-4591 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       64.21         1.74        20.48        24.13         0.56        38.17 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 
       13.12        32.02        19.30         9.57        63.55        14.63 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
       44.25        86.30        71.34        79.20        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
       62.86        56.32        16.64       173.82       151.27        14.07 
TCGA-33-4587 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
       54.44         4.70        36.62         6.94       110.99        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 TCGA-34-5232 
      118.36        27.16         2.63        61.61        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 
       74.66         9.07        60.30        50.66        44.75        39.32 
TCGA-34-5929 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
        4.96        38.79         4.01         0.43         0.39         7.96 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 
        6.81         0.39         3.39        37.58        21.70       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 
      111.35        68.58        55.20        82.52       102.18        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 
        1.94        60.53        36.39        68.38        55.56        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 TCGA-43-6771 
       40.21        38.66        33.11        27.91        21.47         5.46 
TCGA-43-6773 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
        3.81        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3769 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       13.02         4.44        13.91         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-5898 TCGA-56-7223 TCGA-56-7579 
        5.46         8.75        27.45        18.25        14.53        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       30.41        19.76         6.51         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 
       14.96         4.93         3.48        14.07         1.81        22.75 
TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8386 
       10.36        20.25        20.94        13.32         0.26         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.25        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 
       85.12        56.65        29.92        21.11        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       96.82        37.94        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       48.49        42.64        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       70.62        58.65        59.97        45.57        14.99        11.34 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       36.16        53.88        16.96        43.10         2.01        21.07 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        2.01         0.99        43.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
        2.01         2.01         2.01         7.07        23.01        19.00 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 TCGA-66-2787 TCGA-66-2788 
        2.01        19.00        12.00        24.95        40.01        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 
        4.04        22.98        10.06        54.08        49.05         2.73 
TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 
        6.64        13.35        16.18        14.73        12.07        12.33 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       73.12        75.09        23.28        11.18       140.09         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       73.22        70.13       106.95         0.16        46.78        32.55 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 
       86.76        55.73        37.81       156.66        53.92        17.72 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       26.40         6.97        66.51        54.41        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GF TCGA-85-6561 
       36.36       126.18       150.25        22.29        27.62        40.24 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
        6.41        36.53        31.30        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       29.95        25.15        19.04        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       30.64        34.52        10.09        13.22        22.45        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 
        5.29         3.09        32.71        15.39        36.59        38.14 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA 
       18.08        22.59        30.28        34.13        30.97        24.36 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 
       30.48        27.16        16.21        15.85        15.29        29.92 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        3.65        24.92        11.77        22.62        10.59         2.70 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         5.26         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       14.14        71.01        18.31        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 
       30.67        27.02        20.32        18.58        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       13.18        13.41         4.54         1.22        57.30        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
        4.21         2.89        49.28        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        3.65        33.07        43.89        11.18         0.20 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            133.74             173.82 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             19.23              22.98 
[1] "0.1 - 133.7 (19.2)" "0.0 - 173.8 (23.0)"
[1] "hr=" "1"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         0       21       47        1        15        31
  18P LOSS WILD-TYPE       2       68      105        1        50        64
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  18P LOSS MUTATED           2         17          2        5
  18P LOSS WILD-TYPE         1         46         17        2
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 21                 68
  STAGE IB                 47                105
  STAGE II                  1                  1
  STAGE IIA                15                 50
  STAGE IIB                31                 64
  STAGE III                 2                  1
  STAGE IIIA               17                 46
  STAGE IIIB                2                 17
  STAGE IV                  5                  2
[1] 10  2
[1] 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    25  87  22   7
  18P LOSS WILD-TYPE  87 207  49  17
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               25                 87
  T2               87                207
  T3               22                 49
  T4                7                 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
  18P LOSS MUTATED    93  35  10   1
  18P LOSS WILD-TYPE 224  98  30   4
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               93                224
  N1               35                 98
  N2               10                 30
  N3                1                  4
[1] 4 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   115   5
  18P LOSS WILD-TYPE 296   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    115    5
  18P LOSS WILD-TYPE  296    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              115                296
  1                5                  2
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    32 109
  18P LOSS WILD-TYPE  98 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     32  109
  18P LOSS WILD-TYPE   98  262
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               32                 98
  MALE                109                262
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   106  10
  18P LOSS WILD-TYPE 278  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    106   10
  18P LOSS WILD-TYPE  278   43
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO               106                278
  YES               10                 43
[1] 2 2
[1] FALSE
D73V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                       5
  18P LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  18P LOSS MUTATED                                        2
  18P LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                         0
  18P LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                           134
  18P LOSS WILD-TYPE                                                         345
D73V10, multiclass
                                                             clus
vv                                                            18P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              134
                                                             clus
vv                                                            18P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D73V11, continuous
D73V12, continuous
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED   110   3   0   6
  18P LOSS WILD-TYPE 289   9   4  17
D73V13, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              110                289
  R1                3                  9
  R2                0                  4
  RX                6                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       2                        11    94
  18P LOSS WILD-TYPE     7                        20   255
D73V14, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               11                 20
  WHITE                                   94                255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  87
  18P LOSS WILD-TYPE   5 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   87
  18P LOSS WILD-TYPE    5  230
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               87                230
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   115  73
  18Q LOSS WILD-TYPE 165 141
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               188                306 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                73                141 
$`18Q LOSS MUTATED`
TCGA-18-3416 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-A5C4 TCGA-33-4533 
       31.99        32.19        14.93        48.82        22.06       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-43-5668 TCGA-56-7221 TCGA-56-8305 TCGA-56-A4BY 
        1.55        19.76        18.38        19.99         3.45        17.85 
TCGA-56-A5DR TCGA-60-2696 TCGA-63-A5MH TCGA-68-8250 TCGA-90-7766 TCGA-94-7033 
        0.13         3.58        66.61         8.02         9.50        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
        0.16        18.38        16.14        19.36         2.76         5.69 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-18-3412 
        0.07        76.80        39.85        40.90        16.80        11.34 
TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 TCGA-21-1071 TCGA-21-1079 
       23.54        36.07        86.96       119.54        46.88        31.73 
TCGA-21-1080 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-1016 TCGA-22-4593 
      122.43        31.63        33.93        10.82        27.02        35.08 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4613 TCGA-22-5473 TCGA-33-4538 TCGA-33-4547 
       38.17        34.75        11.77        63.55        97.94        79.53 
TCGA-33-4583 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL 
      151.27        63.35         0.30       110.99        44.19        27.16 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5241 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX 
       32.88        65.23        16.93        38.79         4.04        33.90 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-39-5011 TCGA-39-5016 
        0.43         0.39         8.12         7.82       133.25       126.58 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5036 TCGA-43-2576 TCGA-43-3394 TCGA-43-6647 
      102.18         1.71        71.18        40.21        39.12        24.89 
TCGA-43-7656 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-52-7810 TCGA-52-7812 
       19.59         9.83        10.65         0.39        30.35        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7823 
       28.96        12.43        21.90        18.48        14.53        33.24 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 
        3.48        26.89        14.07         1.35        13.81         9.93 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-A46K 
       15.81        19.23        18.74        14.47         0.03        34.36 
TCGA-58-A46M TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 
       35.24        10.22        92.71        21.93        80.45        50.33 
TCGA-60-2720 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MR 
        3.19        11.77       102.67        59.97        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 
       78.28        16.37        53.88        43.10         0.99         1.02 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2773 TCGA-66-2780 
        0.99         2.01         1.02         2.01         3.02        12.03 
TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        3.98         1.97        25.97        22.98         5.03        30.02 
TCGA-66-2795 TCGA-68-7757 TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 TCGA-77-7337 
        4.01         6.94        14.73        12.33        29.56       106.95 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
      156.66        12.59        39.09        17.72       104.09        11.54 
TCGA-77-8144 TCGA-77-8148 TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 
       27.39        66.51       132.36        61.94        38.86         9.67 
TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 TCGA-85-7844 TCGA-85-8049 TCGA-85-8071 
       41.39        34.95        31.30        29.95        19.04        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 
       30.64        34.52         0.76         5.29         3.09         2.01 
TCGA-85-8481 TCGA-85-8584 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 
        7.76        12.59        19.86        30.48        16.21        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
       14.96        15.29        12.39         2.93        11.77        20.22 
TCGA-92-7341 TCGA-92-8063 TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-98-8023 
        3.48         4.01        17.69        18.31        17.46        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J TCGA-L3-A524 TCGA-NC-A5HG 
       27.16        18.15         2.01        20.71        16.11        64.54 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       57.30         4.21        49.28        43.92        25.32        14.73 
TCGA-O2-A52Q TCGA-O2-A52S 
        3.72        12.72 

$`18Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19         4.80         6.18        27.19 
TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
       60.66        64.93       129.01        31.50        28.96        31.27 
TCGA-39-5039 TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
       17.88        22.49         7.76        78.18         2.93        11.61 
TCGA-43-A56V TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-60-2711 
       12.03        13.05        17.00        16.77        21.04        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
        9.01        35.34        32.32        20.78        42.08        30.81 
TCGA-90-7964 TCGA-96-7545 TCGA-98-A53D TCGA-J1-A4AH TCGA-NK-A5CT TCGA-NK-A7XE 
       14.07        57.07        21.21        19.10        65.65         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 
        8.58        75.75       117.57        92.15        92.42         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      154.32        49.94        99.16        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 
       15.58         9.34       119.80        43.23        88.11        41.69 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       21.99         7.33         4.31        64.21         1.74        14.10 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4604 TCGA-22-4605 
       20.48        48.33        24.13         0.56        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       19.30         9.57        14.63        44.25         0.79        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       71.34        79.20        11.74        18.84        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 
       56.32        16.64       173.82       103.53        14.07        54.44 
TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 
        4.70        36.62         6.94       118.36         2.63        61.61 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
       81.24        74.66         9.07        60.30        50.66        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-3783 TCGA-37-4129 
       39.32         4.96         1.12        26.43         4.01         7.96 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN 
        7.46         6.81         0.39         3.39        37.58        21.70 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
      111.35        68.58        55.20        82.52        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 
       60.53        36.39        68.38        55.56        17.06        38.66 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       33.11        27.91        22.98        21.47         5.46         3.81 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3769 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       13.02         4.44        13.91         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
        5.46         8.75        18.25        31.27        30.41        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 TCGA-56-8622 
        6.51         0.10        17.49        14.96         4.93         1.81 
TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A5DS 
       22.75        10.36        20.25        20.94        13.32         0.26 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.25        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 
       85.12        56.65        29.92        21.11        12.23        96.82 
TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2719 
       37.94        49.48        66.54        56.91        48.49        42.64 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 
       29.85        35.90        23.57        26.83        52.67        70.13 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5ML 
       70.42        68.15        55.30        70.62        58.65        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2737 
       14.99        11.34        36.16        34.59        16.96         2.01 
TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
       21.07         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 
       25.05         2.01         7.07        23.01        19.00         2.01 
TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       19.00        12.00        24.95        40.01        22.98         4.04 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 
       10.06        54.08        49.05         2.73         6.64        13.35 
TCGA-68-A59I TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       16.18        12.07        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 
      140.09         0.49        73.22        70.13         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 
       32.55         6.51        86.76        55.73        37.81        53.92 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
       26.40         6.97        54.41        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-6561 
      126.18       150.25        22.29         5.92        27.62        40.24 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 
        6.41        36.53        32.91         1.38         1.15        18.94 
TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 
       25.15        24.13        31.56        10.09        13.22        22.45 
TCGA-85-8351 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
       16.77        32.71        15.39        36.59        38.14        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR 
       22.59        30.28        34.13        30.97        24.36        19.73 
TCGA-85-A50M TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-A4EE TCGA-90-A59Q 
       27.16        29.92         3.65        24.92        22.62        10.59 
TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        2.70         5.26         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       14.14        71.01        27.68        21.44        30.81        30.67 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW 
       27.02        20.32        18.58        12.89        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HT 
       11.84         4.54         1.22        13.74         2.89        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       83.57         3.65        33.07        43.89        11.18         0.20 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.03               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            156.66             173.82 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            19.675             22.865 
[1] "0.0 - 156.7 (19.7)" "0.1 - 173.8 (22.9)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         0       27       58        0        26        43
  18Q LOSS WILD-TYPE       2       62       94        2        39        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  18Q LOSS MUTATED           2         25          2        5
  18Q LOSS WILD-TYPE         1         38         17        2
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 27                 62
  STAGE IB                 58                 94
  STAGE II                  0                  2
  STAGE IIA                26                 39
  STAGE IIB                43                 52
  STAGE III                 2                  1
  STAGE IIIA               25                 38
  STAGE IIIB                2                 17
  STAGE IV                  5                  2
[1] 10  2
[1] 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    36 114  33   7
  18Q LOSS WILD-TYPE  76 180  38  17
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               36                 76
  T2              114                180
  T3               33                 38
  T4                7                 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
  18Q LOSS MUTATED   116  57  13   1
  18Q LOSS WILD-TYPE 201  76  27   4
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              116                201
  N1               57                 76
  N2               13                 27
  N3                1                  4
[1] 4 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   151   5
  18Q LOSS WILD-TYPE 260   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    151    5
  18Q LOSS WILD-TYPE  260    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              151                260
  1                5                  2
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    46 144
  18Q LOSS WILD-TYPE  84 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     46  144
  18Q LOSS WILD-TYPE   84  227
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               46                 84
  MALE                144                227
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   147  16
  18Q LOSS WILD-TYPE 237  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    147   16
  18Q LOSS WILD-TYPE  237   37
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               147                237
  YES               16                 37
[1] 2 2
[1] FALSE
D74V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                       5
  18Q LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  18Q LOSS MUTATED                                        3
  18Q LOSS WILD-TYPE                                      3
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                         0
  18Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                           182
  18Q LOSS WILD-TYPE                                                         297
D74V10, multiclass
                                                             clus
vv                                                            18Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              182
                                                             clus
vv                                                            18Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                297
[1] 4 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   152   3   0  12
  18Q LOSS WILD-TYPE 247   9   4  11
D74V13, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              152                247
  R1                3                  9
  R2                0                  4
  RX               12                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       3                        15   132
  18Q LOSS WILD-TYPE     6                        16   217
D74V14, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN               15                 16
  WHITE                                  132                217
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4 122
  18Q LOSS WILD-TYPE   4 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4  122
  18Q LOSS WILD-TYPE    4  195
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              122                195
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    94  68
  19P LOSS WILD-TYPE 186 146
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               162                332 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                68                146 
$`19P LOSS MUTATED`
TCGA-18-3409 TCGA-21-A5DI TCGA-22-A5C4 TCGA-33-4532 TCGA-34-2604 TCGA-43-2578 
      123.19        32.19        22.06       129.01        31.50        22.49 
TCGA-43-5668 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 TCGA-56-A4ZJ 
       18.38        11.61        12.03        19.99         3.45        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-68-8250 TCGA-90-7964 TCGA-94-7557 
        0.13         3.58        41.42         8.02        14.07         0.16 
TCGA-94-7943 TCGA-98-A539 TCGA-NC-A5HD TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3412 
       18.38         5.69         0.07        65.65        16.80        11.34 
TCGA-18-3417 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1077 TCGA-21-1081 
       36.07        49.94       119.54        46.88        34.78         9.34 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 
       43.23        88.11        33.93        21.99         4.31        64.21 
TCGA-22-4594 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-5485 TCGA-22-5492 
       48.33        34.75        32.02        19.30        30.12        16.64 
TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-33-AASB TCGA-33-AASI TCGA-34-2608 
      103.53        54.44        63.35         6.94        44.19        32.88 
TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 TCGA-34-8456 TCGA-37-3792 TCGA-37-4129 
       16.93        39.32         4.96        26.43         0.39         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        8.12         7.46         7.82         6.81         0.39         3.39 
TCGA-37-A5EN TCGA-39-5011 TCGA-39-5029 TCGA-39-5036 TCGA-43-2576 TCGA-43-3394 
       21.70       133.25        24.33        71.18        40.21        39.12 
TCGA-43-5670 TCGA-43-6771 TCGA-43-7656 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       27.91         5.46        19.59         4.44        10.65        13.91 
TCGA-51-4081 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7222 
       29.95         8.75        28.96        12.43        18.25        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       14.53        31.27         6.51        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8624 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A62T 
        4.93        13.81        15.81        20.94        13.32        14.47 
TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46L TCGA-60-2706 TCGA-60-2707 
        0.03        13.55        29.95        56.65        92.71        21.93 
TCGA-60-2714 TCGA-60-2722 TCGA-60-2723 TCGA-63-6202 TCGA-63-7020 TCGA-63-7023 
       50.33        29.85        35.90        52.67        70.13        55.30 
TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-66-2727 
       58.65        25.28        89.29        78.28        36.16        16.96 
TCGA-66-2753 TCGA-66-2756 TCGA-66-2759 TCGA-66-2769 TCGA-66-2780 TCGA-66-2781 
        1.02         0.99        25.05         7.07        12.03         3.98 
TCGA-66-2782 TCGA-66-2786 TCGA-66-2788 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 
       12.00        25.97        22.98        10.06         4.01         2.73 
TCGA-68-7756 TCGA-70-6723 TCGA-77-6845 TCGA-77-7138 TCGA-77-7338 TCGA-77-7463 
        6.64        12.33        23.28        11.18         0.16        46.78 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8156 
       39.09        17.72        26.40        27.39         6.97        36.36 
TCGA-85-6560 TCGA-85-7697 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
       41.39        34.95        31.56        30.64        34.52         0.76 
TCGA-85-8351 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A510 
       16.77        12.59        30.28        30.97        19.86        15.85 
TCGA-85-A53L TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-94-A4VJ TCGA-94-A5I6 
       12.39        20.22         3.48         4.01        14.14        17.69 
TCGA-96-8169 TCGA-98-A53A TCGA-98-A53B TCGA-L3-A524 TCGA-NC-A5HG TCGA-NC-A5HI 
       18.31        18.15         2.01        16.11        64.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-O2-A52N TCGA-O2-A52Q 
       13.74         4.21        25.32        14.73        33.07         3.72 

$`19P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 
       14.93        48.82        60.66        64.93       133.74         1.55 
TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-7657 TCGA-43-7658 
       19.76        28.96        31.27        17.88         7.76        78.18 
TCGA-43-8118 TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2712 
        2.93        13.05        17.00        16.77        17.85         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32        66.61        20.78        42.08        30.81 
TCGA-90-7766 TCGA-94-7033 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
        9.50        21.04        16.14        57.07        19.36         2.76 
TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE 
       21.21        19.10        76.80        39.85        40.90         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 
        8.58        75.75       117.57        23.54        92.15        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
       86.96         2.79       154.32        99.16        70.16        60.89 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 
       15.58        31.73       122.43       119.80        31.63        41.69 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
       10.82         7.33         1.74        14.10        27.02        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4609 
       35.08        24.13         0.56        38.17        13.12         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       11.77        63.55        14.63        44.25         0.79        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 
       71.34        79.20        11.74        18.84        62.86        56.32 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN 
       97.94        79.53       173.82       151.27        14.07         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
        0.30        36.62       110.99       118.36        27.16         2.63 
TCGA-34-2600 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       61.61        65.23        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5927 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX 
       50.66        44.75         1.12        38.79         4.04        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-A5EL TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        4.01         0.43        37.58       126.58       111.35        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 
       55.20        82.52       102.18         1.71         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-3920 
       36.39        68.38        55.56        17.06        38.66        33.11 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-8115 TCGA-43-8116 
       22.98        24.89        21.47         3.81        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
        9.73        14.20        13.32        12.16        13.02         9.83 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 
        0.39         0.39        28.34         5.46        30.35        27.45 
TCGA-56-6545 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
       21.90        30.41        19.76         0.10         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 
       14.07         1.35         1.81        22.75        10.36         9.93 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 TCGA-58-8391 
       20.25        19.23        18.74         0.26        13.25        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N 
       16.47        34.78        85.12        34.36        35.24        29.92 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 
       21.11        12.23        10.22        96.82        37.94        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       49.48        66.54        56.91        48.49        42.64         3.19 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB 
       23.57        26.83        11.77        70.42        68.15       102.67 
TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MT 
       70.62        59.97        45.57        14.99        11.34        16.37 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       53.88        34.59        43.10         2.01        21.07         0.99 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 
        2.01         0.92        43.99        21.01         0.99         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
        1.02         2.01         2.01        23.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2789 
        2.01        19.00        24.95         1.97        40.01         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7757 
       22.98         5.03        30.02        54.08        49.05         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 
       13.35        16.18        14.73        12.07        29.56        73.12 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       75.09       140.09         0.49        73.22        70.13       106.95 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       32.55         6.51        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8148 TCGA-77-8150 
       12.59        53.92       104.09        11.54        66.51        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
       65.49        60.53       126.18       132.36       150.25        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 
        5.92        61.94        27.62        38.86         9.67        40.24 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
        6.41        36.53        31.30        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
       29.95        18.94        25.15        19.04        24.13        26.79 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       10.09        13.22        22.45         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
        2.01        15.39         7.76        36.59        38.14        18.08 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       22.59        34.13        24.36        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 
       16.21        14.96        15.29        29.92         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 
        2.93        11.77        22.62        10.59         2.70         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-8170 
        2.30         4.01         5.03        26.63        71.01        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       27.68        21.44        30.81        30.67        21.34        27.16 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A446 
       27.02        20.32        18.58        20.71        12.89        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HL TCGA-NC-A5HN 
       13.41        11.84         4.54         1.22         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V 
       43.92        26.43        83.57         3.65        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.03               0.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            133.25             173.82 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            19.445             22.980 
[1] "0.0 - 133.2 (19.4)" "0.1 - 173.8 (23.0)"
[1] "hr=" "1.2"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         1       28       49        0        26        25
  19P LOSS WILD-TYPE       1       61      103        2        39        70
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  19P LOSS MUTATED           1         21          6        4
  19P LOSS WILD-TYPE         2         42         13        3
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 28                 61
  STAGE IB                 49                103
  STAGE II                  0                  2
  STAGE IIA                26                 39
  STAGE IIB                25                 70
  STAGE III                 1                  2
  STAGE IIIA               21                 42
  STAGE IIIB                6                 13
  STAGE IV                  4                  3
[1] 10  2
[1] 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    37  95  20  10
  19P LOSS WILD-TYPE  75 199  51  14
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               37                 75
  T2               95                199
  T3               20                 51
  T4               10                 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
  19P LOSS MUTATED   112  32  16   0
  19P LOSS WILD-TYPE 205 101  24   5
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0              112                205
  N1               32                101
  N2               16                 24
  N3                0                  5
[1] 4 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   133   4
  19P LOSS WILD-TYPE 278   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    133    4
  19P LOSS WILD-TYPE  278    3
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              133                278
  1                4                  3
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    37 125
  19P LOSS WILD-TYPE  93 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     37  125
  19P LOSS WILD-TYPE   93  246
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               37                 93
  MALE                125                246
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   119  21
  19P LOSS WILD-TYPE 265  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    119   21
  19P LOSS WILD-TYPE  265   32
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO               119                265
  YES               21                 32
[1] 2 2
[1] FALSE
D75V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                       5
  19P LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  19P LOSS MUTATED                                        2
  19P LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                         1
  19P LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                           154
  19P LOSS WILD-TYPE                                                         325
D75V10, multiclass
                                                             clus
vv                                                            19P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              154
                                                             clus
vv                                                            19P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D75V11, continuous
D75V12, continuous
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED   124   6   1   7
  19P LOSS WILD-TYPE 275   6   3  16
D75V13, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0              124                275
  R1                6                  6
  R2                1                  3
  RX                7                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       2                        11   115
  19P LOSS WILD-TYPE     7                        20   234
D75V14, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               11                 20
  WHITE                                  115                234
[1] 3 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     3 108
  19P LOSS WILD-TYPE   5 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3  108
  19P LOSS WILD-TYPE    5  209
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO              108                209
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    67  43
  19Q LOSS WILD-TYPE 213 171
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               110                384 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                43                171 
$`19Q LOSS MUTATED`
TCGA-18-3409 TCGA-18-3416 TCGA-21-A5DI TCGA-22-A5C4 TCGA-33-4532 TCGA-43-A474 
      123.19        31.99        32.19        22.06       129.01        11.61 
TCGA-56-7221 TCGA-56-8305 TCGA-60-2696 TCGA-68-8250 TCGA-94-7943 TCGA-98-A539 
       19.99         3.45         3.58         8.02        18.38         5.69 
TCGA-NC-A5HD TCGA-NK-A5D1 TCGA-18-3412 TCGA-18-5592 TCGA-21-1077 TCGA-22-0940 
        0.07        16.80        11.34        49.94        34.78        21.99 
TCGA-22-0944 TCGA-22-1005 TCGA-22-4594 TCGA-22-4607 TCGA-22-4613 TCGA-33-4586 
        7.33        64.21        48.33        19.30        11.77        14.07 
TCGA-33-4587 TCGA-33-AASB TCGA-34-5929 TCGA-34-8456 TCGA-37-4129 TCGA-37-4133 
       54.44         6.94         4.96        26.43         7.96         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5036 TCGA-43-3394 
        6.81         0.39        37.58        21.70        71.18        39.12 
TCGA-43-6771 TCGA-43-7656 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 
        5.46        19.59         4.44        10.65        13.91        29.95 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7222 
       30.35         8.75        28.96        12.43        18.25        18.48 
TCGA-56-7579 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-A4BX TCGA-56-A62T 
       31.27        17.49        33.24        14.96        13.32        14.47 
TCGA-58-8386 TCGA-58-A46L TCGA-60-2706 TCGA-60-2707 TCGA-60-2714 TCGA-63-6202 
        0.03        56.65        92.71        21.93        50.33        52.67 
TCGA-63-7023 TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MS TCGA-66-2727 TCGA-66-2753 
       55.30        58.65        25.28        78.28        16.96         1.02 
TCGA-66-2756 TCGA-66-2759 TCGA-66-2781 TCGA-66-2786 TCGA-66-2794 TCGA-66-2795 
        0.99        25.05         3.98        25.97        54.08         4.01 
TCGA-68-7755 TCGA-68-7756 TCGA-70-6723 TCGA-77-6845 TCGA-77-7338 TCGA-77-7463 
        2.73         6.64        12.33        23.28         0.16        46.78 
TCGA-77-8136 TCGA-77-8143 TCGA-77-8144 TCGA-77-8156 TCGA-85-6560 TCGA-85-6561 
       39.09        26.40        27.39        36.36        41.39        40.24 
TCGA-85-7697 TCGA-85-7843 TCGA-85-7950 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
       34.95         1.15        18.94        31.56        26.79        30.64 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8351 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JC 
       34.52         0.76        16.77        12.59        30.28        19.86 
TCGA-85-A512 TCGA-90-A4ED TCGA-92-8063 TCGA-94-A4VJ TCGA-98-A53A TCGA-L3-A524 
       15.29        20.22         4.01        14.14        18.15        16.11 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HP 
       11.84        64.54        57.30        13.74         4.21        25.32 
TCGA-O2-A52N TCGA-O2-A52Q 
       33.07         3.72 

$`19Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 
       12.20         4.47         4.80         6.18        27.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 
       48.82        60.66        64.93       133.74         1.55        19.76 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 
       31.50        28.96        31.27        17.88        22.49        18.38 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56V TCGA-56-8201 TCGA-56-8308 
        7.76        78.18         2.93        12.03        13.05        17.00 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 
       16.77        17.85        21.04         0.13        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32        66.61        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-7545 
        9.50        14.07        21.04         0.16        16.14        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HM 
       19.36         2.76        21.21        19.10        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       40.90        65.65         0.43         8.58        75.75       117.57 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       23.54        92.15        36.07        92.42        86.96         2.79 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
      154.32       119.54        46.88        99.16        70.16        60.89 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       15.58        31.73       122.43         9.34       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 
       31.63        88.11        41.69        33.93        10.82         4.31 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
        1.74        14.10        27.02        20.48        35.08        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 
        0.56        38.17        34.75        13.12        32.02         9.57 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       63.55        14.63        44.25         0.79        86.30        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       16.64        97.94        79.53       173.82       103.53       151.27 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI 
       63.35         4.70         0.30        36.62       110.99        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
      118.36        27.16         2.63        61.61        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       81.24        74.66         9.07        60.30        50.66        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX 
       44.75        39.32         1.12        38.79         4.04        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 
        4.01         0.43         0.39         8.12         7.46         3.39 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
      133.25       126.58       111.35        68.58        55.20        82.52 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
      102.18         1.71        24.33         1.94        60.53        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 
       68.38        55.56        17.06        40.21        38.66        33.11 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-8115 
       27.91        22.98        24.89        21.47         3.81        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       11.77         9.73        14.20        13.32        12.16        13.02 
TCGA-46-3768 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 
        9.83         0.39         0.39        28.34         5.46        27.45 
TCGA-56-6545 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       21.90        14.53        30.41        19.76         6.51         0.10 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        4.93         3.48        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 
       20.94        19.23        18.74         0.26        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       35.24        29.92        21.11        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 
       37.94        80.45        49.48        66.54        56.91        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG 
       11.77        70.13        70.42        68.15       102.67        70.62 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MT 
       59.97        45.57        14.99        11.34        89.29        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       36.16        53.88        34.59        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 
        0.99         2.01         0.92        43.99        21.01         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
        2.01         1.02         2.01         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
       19.00         3.02         2.01        19.00        12.03        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       24.95         1.97        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7757 TCGA-68-8251 
        5.03        30.02        10.06        49.05         6.94        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       16.18        14.73        12.07        29.56        73.12        75.09 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       11.18       140.09         0.49        73.22        70.13       106.95 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       32.55         6.51        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 
       12.59        53.92        17.72       104.09        11.54         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       66.51        54.41        65.49        60.53       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH 
      150.25        22.29         5.92        61.94        27.62        38.86 
TCGA-85-6175 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
        9.67         6.41        36.53        31.30        32.91         1.38 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8277 TCGA-85-8288 
       29.95        25.15        19.04        24.13        10.09        13.22 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       22.45         5.29         3.09        32.71         2.01        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN 
        7.76        36.59        38.14        18.08        22.59        34.13 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       30.97        24.36        30.48        19.73        27.16        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       15.85        14.96        29.92        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
        2.93        11.77        22.62        10.59         2.70         3.48 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 
        5.26         2.30         4.01         5.03        26.63        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       71.01        18.31        17.46        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       30.67        21.34        27.16         2.01        27.02        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF 
       18.58        20.71        12.89        13.18        13.41         4.54 
TCGA-NC-A5HH TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT 
        1.22         2.89        49.28        43.92        14.73        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       83.57         3.65        12.72        43.89        11.18         0.20 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.03               0.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            129.01             173.82 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            19.445             22.605 
[1] "0.0 - 129.0 (19.4)" "0.1 - 173.8 (22.6)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         1       17       32        0        22        19
  19Q LOSS WILD-TYPE       1       72      120        2        43        76
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  19Q LOSS MUTATED           1         11          4        2
  19Q LOSS WILD-TYPE         2         52         15        5
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 17                 72
  STAGE IB                 32                120
  STAGE II                  0                  2
  STAGE IIA                22                 43
  STAGE IIB                19                 76
  STAGE III                 1                  2
  STAGE IIIA               11                 52
  STAGE IIIB                4                 15
  STAGE IV                  2                  5
[1] 10  2
[1] 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    25  63  15   7
  19Q LOSS WILD-TYPE  87 231  56  17
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               25                 87
  T2               63                231
  T3               15                 56
  T4                7                 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
  19Q LOSS MUTATED    71  26  10   0
  19Q LOSS WILD-TYPE 246 107  30   5
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               71                246
  N1               26                107
  N2               10                 30
  N3                0                  5
[1] 4 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    92   2
  19Q LOSS WILD-TYPE 319   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     92    2
  19Q LOSS WILD-TYPE  319    5
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               92                319
  1                2                  5
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    21  89
  19Q LOSS WILD-TYPE 109 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     21   89
  19Q LOSS WILD-TYPE  109  282
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               21                109
  MALE                 89                282
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    77  18
  19Q LOSS WILD-TYPE 307  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     77   18
  19Q LOSS WILD-TYPE  307   35
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                77                307
  YES               18                 35
[1] 2 2
[1] FALSE
D76V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED                                       4
  19Q LOSS WILD-TYPE                                    11
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  19Q LOSS MUTATED                                        2
  19Q LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED                                         1
  19Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                           103
  19Q LOSS WILD-TYPE                                                         376
D76V10, multiclass
                                                             clus
vv                                                            19Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              103
                                                             clus
vv                                                            19Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                376
[1] 4 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    81   3   1   6
  19Q LOSS WILD-TYPE 318   9   3  17
D76V13, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               81                318
  R1                3                  9
  R2                1                  3
  RX                6                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         7    80
  19Q LOSS WILD-TYPE     8                        24   269
D76V14, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                7                 24
  WHITE                                   80                269
[1] 3 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  72
  19Q LOSS WILD-TYPE   6 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   72
  19Q LOSS WILD-TYPE    6  245
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               72                245
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    25  17
  20P LOSS WILD-TYPE 255 197
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                452 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                17                197 
$`20P LOSS MUTATED`
TCGA-18-3416 TCGA-60-2712 TCGA-63-A5MH TCGA-NC-A5HM TCGA-18-4721 TCGA-21-1078 
       31.99         9.01        66.61        39.85       154.32        15.58 
TCGA-21-5787 TCGA-22-4593 TCGA-22-5478 TCGA-33-4583 TCGA-33-4586 TCGA-33-AASB 
       10.82        35.08         0.79       151.27        14.07         6.94 
TCGA-37-3792 TCGA-37-4135 TCGA-39-5034 TCGA-43-3394 TCGA-43-6771 TCGA-52-7810 
        0.39         6.81        36.39        39.12         5.46        30.35 
TCGA-56-8307 TCGA-60-2706 TCGA-60-2714 TCGA-66-2755 TCGA-66-2766 TCGA-66-2768 
       26.89        92.71        50.33         0.92         1.02         2.01 
TCGA-66-2790 TCGA-66-2791 TCGA-68-A59J TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 
       22.98         5.03        14.73       106.95        46.78        32.55 
TCGA-77-8144 TCGA-85-6560 TCGA-85-7950 TCGA-85-8071 TCGA-85-8352 TCGA-85-A4QR 
       27.39        41.39        18.94        26.79         5.29        19.73 
TCGA-85-A50Z TCGA-92-8065 TCGA-96-7544 TCGA-96-8169 TCGA-98-A538 TCGA-NC-A5HG 
       16.21         2.30        71.01        18.31        27.16        64.54 

$`20P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19         4.80         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
      129.01       133.74         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       31.27        17.88        22.49        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
        2.93        11.61        12.03        19.99        13.05         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       17.00        16.77        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
       41.42        35.34        32.32         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       30.81         9.50        14.07        21.04         0.16        18.38 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D 
       16.14        57.07        19.36         2.76         5.69        21.21 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
       19.10         0.07        76.80        40.90        65.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        0.43         8.58        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 
       92.15        36.07        92.42        86.96         2.79        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      119.54        46.88        99.16        70.16        60.89        34.78 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       31.73       122.43         9.34       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       88.11        41.69        33.93        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
       64.21         1.74        14.10        27.02        20.48        48.33 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       24.13         0.56        38.17        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       19.30         9.57        11.77        63.55        14.63        44.25 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       86.30        71.34        79.20        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        56.32        16.64        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      103.53        54.44        63.35         4.70         0.30        36.62 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
      110.99        44.19       118.36        27.16         2.63        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       32.88        65.23        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       50.66        16.93        44.75        39.32         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       38.79         4.04        26.43        33.90         4.01         0.43 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 
        7.96         8.12         7.46         7.82         0.39         3.39 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
       37.58        21.70       133.25       126.58       111.35        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        82.52       102.18         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       60.53        68.38        71.18        55.56        17.06        40.21 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       38.66        33.11        27.91        22.98        24.89        21.47 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        3.81        19.59        13.38        11.77         9.73        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
       13.32        12.16        13.02         9.83         4.44        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       13.91         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        8.75        27.45        28.96        12.43        18.25        21.90 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
       18.48        14.53        31.27        30.41        19.76         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 
        0.10        17.49        33.24        14.96         4.93         3.48 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
        9.93        20.25        15.81        20.94        19.23        13.32 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.26        14.47         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 
       56.65        35.24        29.92        21.11        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       96.82        37.94        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       56.91        48.49        42.64         3.19        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
       23.57        26.83        11.77        52.67        70.13        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       68.15        55.30       102.67        70.62        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       45.57        14.99        11.34        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       16.37        36.16        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
        2.01        21.07         0.99         1.02         2.01         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
       43.99        21.01        25.05         0.99         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        7.07        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       12.03         3.98        12.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
       40.01        22.98         4.04        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
        4.01        49.05         2.73         6.64         6.94        13.35 
TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       16.18        12.07        12.33        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       23.28        11.18       140.09         0.49        73.22        70.13 
TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        0.16         6.51        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       12.59        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       26.40         6.97        66.51        54.41        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       36.36       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 
       61.94        27.62        38.86         9.67        40.24         6.41 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       36.53        34.95        31.30        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
       29.95        25.15        19.04        24.13        31.56        30.64 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       34.52        10.09         0.76        13.22        22.45        16.77 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        3.09        32.71         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       38.14        12.59        18.08        22.59        30.28        34.13 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A510 
       30.97        19.86        24.36        30.48        27.16        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       14.96        15.29        29.92        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        2.93        11.77        20.22        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        3.48         4.01         5.26         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       14.14        17.69        17.46        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       30.67        21.34        18.15         2.01        27.02        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       18.58        20.71        12.89        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
       11.84         4.54         1.22        57.30        13.74         4.21 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
        2.89        49.28        43.92        25.32        14.73        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       83.57         3.65        33.07         3.72        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.39               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            154.32             173.82 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            24.885             21.585 
[1] "0.4 - 154.3 (24.9)" "0.0 - 173.8 (21.6)"
[1] "hr=" "1.1"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         0        5       14        0         5        12
  20P LOSS WILD-TYPE       2       84      138        2        60        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  20P LOSS MUTATED           0          5          1        0
  20P LOSS WILD-TYPE         3         58         18        7
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                 84
  STAGE IB                 14                138
  STAGE II                  0                  2
  STAGE IIA                 5                 60
  STAGE IIB                12                 83
  STAGE III                 0                  3
  STAGE IIIA                5                 58
  STAGE IIIB                1                 18
  STAGE IV                  0                  7
[1] 10  2
[1] 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     7  29   6   0
  20P LOSS WILD-TYPE 105 265  65  24
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                7                105
  T2               29                265
  T3                6                 65
  T4                0                 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                  N0  N1  N2  N3
  20P LOSS MUTATED    26  11   4   1
  20P LOSS WILD-TYPE 291 122  36   4
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               26                291
  N1               11                122
  N2                4                 36
  N3                1                  4
[1] 4 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    37   0
  20P LOSS WILD-TYPE 374   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     37    0
  20P LOSS WILD-TYPE  374    7
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               37                374
  1                0                  7
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8  34
  20P LOSS WILD-TYPE 122 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   34
  20P LOSS WILD-TYPE  122  337
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                122
  MALE                 34                337
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    31   4
  20P LOSS WILD-TYPE 353  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     31    4
  20P LOSS WILD-TYPE  353   49
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                31                353
  YES                4                 49
[1] 2 2
[1] FALSE
D77V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED                                       1
  20P LOSS WILD-TYPE                                    14
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  20P LOSS MUTATED                                        0
  20P LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED                                         0
  20P LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                            41
  20P LOSS WILD-TYPE                                                         438
D77V10, multiclass
                                                             clus
vv                                                            20P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               41
                                                             clus
vv                                                            20P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                438
[1] 4 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    33   1   0   3
  20P LOSS WILD-TYPE 366  11   4  20
D77V13, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               33                366
  R1                1                 11
  R2                0                  4
  RX                3                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         3    30
  20P LOSS WILD-TYPE     9                        28   319
D77V14, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                   30                319
[1] 3 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     0  26
  20P LOSS WILD-TYPE   8 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   26
  20P LOSS WILD-TYPE    8  291
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               26                291
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    24  24
  20Q LOSS WILD-TYPE 256 190
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                48                446 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                24                190 
$`20Q LOSS MUTATED`
TCGA-18-3416 TCGA-56-8308 TCGA-60-2712 TCGA-63-A5MH TCGA-96-A4JK TCGA-18-3411 
       31.99        17.00         9.01        66.61        19.36       117.57 
TCGA-18-3415 TCGA-18-4721 TCGA-21-1078 TCGA-22-4604 TCGA-22-5478 TCGA-33-4583 
       92.15       154.32        15.58        13.12         0.79       151.27 
TCGA-33-4586 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2600 TCGA-34-7107 TCGA-39-5021 
       14.07         6.94       118.36        61.61         1.12        68.58 
TCGA-39-5034 TCGA-43-3394 TCGA-43-6771 TCGA-46-6025 TCGA-52-7622 TCGA-56-7580 
       36.39        39.12         5.46        10.65        28.34        30.41 
TCGA-56-8307 TCGA-58-8392 TCGA-60-2698 TCGA-60-2704 TCGA-60-2723 TCGA-66-2755 
       26.89        16.47        10.22        37.94        35.90         0.92 
TCGA-66-2766 TCGA-66-2791 TCGA-68-A59J TCGA-77-7142 TCGA-77-8144 TCGA-77-8153 
        1.02         5.03        14.73        73.22        27.39        65.49 
TCGA-77-8156 TCGA-85-7698 TCGA-85-7950 TCGA-85-8071 TCGA-85-8352 TCGA-85-A4CN 
       36.36        31.30        18.94        26.79         5.29        34.13 
TCGA-85-A50Z TCGA-92-8065 TCGA-96-7544 TCGA-L3-A524 TCGA-NC-A5HL TCGA-NC-A5HN 
       16.21         2.30        71.01        16.11         2.89        49.28 

$`20Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19         4.80         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
      129.01       133.74         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       31.27        17.88        22.49        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
        2.93        11.61        12.03        19.99        13.05         3.45 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       16.77        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32         8.02        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        9.50        14.07        21.04         0.16        18.38        16.14 
TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       57.07         2.76         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE 
       76.80        39.85        40.90        65.65        16.80         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 
        8.58        75.75        11.34        23.54        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
       86.96         2.79        49.94       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       70.16        60.89        34.78        31.73       122.43         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
      119.80        43.23        31.63        88.11        41.69        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       10.82        21.99         7.33         4.31        64.21         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
       14.10        27.02        20.48        35.08        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
        0.56        38.17        34.75        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
       11.77        63.55        14.63        44.25        86.30        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 
       16.64        97.94        79.53       173.82       103.53        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI 
       63.35         4.70         0.30        36.62       110.99        44.19 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       27.16         2.63        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        60.30        50.66        16.93        44.75        39.32 
TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        4.96        38.79         4.04        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         7.96         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        6.81         0.39         3.39        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      126.58       111.35        55.20        82.52       102.18         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
       24.33         1.94        60.53        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       17.06        40.21        38.66        33.11        27.91        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       24.89        21.47         3.81        19.59        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
        9.73        14.20        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 
        4.44        13.91         0.39         0.39        29.95         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       30.35         8.75        27.45        28.96        12.43        18.25 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
       21.90        18.48        14.53        31.27        19.76         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 
        0.10        17.49        33.24        14.96         4.93         3.48 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
        9.93        20.25        15.81        20.94        19.23        13.32 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.26        14.47         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       29.95        71.24        34.78        85.12        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2706 
       35.24        29.92        21.11        12.23        96.82        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       21.93        80.45        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 
       48.49        42.64         3.19        29.85        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       11.34        25.28        89.29        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       53.88        34.59        16.96        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        0.99         1.02         2.01         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       25.05         0.99         2.01         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
       23.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        3.98        12.00        24.95         1.97        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
       22.98         4.04        22.98        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
        4.01        49.05         2.73         6.64         6.94        13.35 
TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       16.18        12.07        12.33        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       23.28        11.18       140.09         0.49        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        0.16        46.78        32.55         6.51        86.76        55.73 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       37.81       156.66        12.59        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
      104.09        11.54        26.40         6.97        66.51        54.41 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       60.53       126.18       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       61.94        27.62        38.86         9.67        41.39        40.24 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
        6.41        36.53        34.95        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
       29.95        25.15        19.04        24.13        31.56        30.64 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       34.52        10.09         0.76        13.22        22.45        16.77 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        3.09        32.71         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB 
       38.14        12.59        18.08        22.59        30.28        30.97 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 
       19.86        24.36        30.48        19.73        27.16        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       14.96        15.29        29.92        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        2.93        11.77        20.22        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        3.48         4.01         5.26         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       14.14        17.69        18.31        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B 
       30.81        30.67        21.34        27.16        18.15         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A446 
       27.02        20.32        18.58        20.71        12.89        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       13.41        11.84         4.54        64.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
       13.74         4.21        43.92        25.32        14.73        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       83.57         3.65        33.07         3.72        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.79               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            154.32             173.82 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            26.840             21.585 
[1] "0.8 - 154.3 (26.8)" "0.0 - 173.8 (21.6)"
[1] "hr=" "1"  
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         0        6       19        1         6        12
  20Q LOSS WILD-TYPE       2       83      133        1        59        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  20Q LOSS MUTATED           0          4          1        0
  20Q LOSS WILD-TYPE         3         59         18        7
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  6                 83
  STAGE IB                 19                133
  STAGE II                  1                  1
  STAGE IIA                 6                 59
  STAGE IIB                12                 83
  STAGE III                 0                  3
  STAGE IIIA                4                 59
  STAGE IIIB                1                 18
  STAGE IV                  0                  7
[1] 10  2
[1] 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     7  36   6   0
  20Q LOSS WILD-TYPE 105 258  65  24
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                7                105
  T2               36                258
  T3                6                 65
  T4                0                 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                  N0  N1  N2  N3
  20Q LOSS MUTATED    33  12   3   1
  20Q LOSS WILD-TYPE 284 121  37   4
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0               33                284
  N1               12                121
  N2                3                 37
  N3                1                  4
[1] 4 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    42   0
  20Q LOSS WILD-TYPE 369   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     42    0
  20Q LOSS WILD-TYPE  369    7
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0               42                369
  1                0                  7
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    13  36
  20Q LOSS WILD-TYPE 117 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     13   36
  20Q LOSS WILD-TYPE  117  335
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               13                117
  MALE                 36                335
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    41   4
  20Q LOSS WILD-TYPE 343  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     41    4
  20Q LOSS WILD-TYPE  343   49
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                41                343
  YES                4                 49
[1] 2 2
[1] FALSE
D78V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                    15
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  20Q LOSS MUTATED                                        0
  20Q LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED                                         0
  20Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q LOSS MUTATED                                                            49
  20Q LOSS WILD-TYPE                                                         430
D78V10, multiclass
                                                             clus
vv                                                            20Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               49
                                                             clus
vv                                                            20Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       15
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                430
[1] 4 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    40   2   0   4
  20Q LOSS WILD-TYPE 359  10   4  19
D78V13, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               40                359
  R1                2                 10
  R2                0                  4
  RX                4                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         3    34
  20Q LOSS WILD-TYPE     9                        28   315
D78V14, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                   34                315
[1] 3 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     1  30
  20Q LOSS WILD-TYPE   7 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   30
  20Q LOSS WILD-TYPE    7  287
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               30                287
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   149 112
  21Q LOSS WILD-TYPE 131 102
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               261                233 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               112                102 
$`21Q LOSS MUTATED`
TCGA-18-3416 TCGA-18-4083 TCGA-22-1017 TCGA-22-5471 TCGA-33-4532 TCGA-33-4589 
       31.99         6.18        48.82        60.66       129.01         1.55 
TCGA-34-2604 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-8118 TCGA-43-A56V 
       31.50        17.88        22.49        18.38         2.93        12.03 
TCGA-56-8305 TCGA-56-A4ZJ TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 
        3.45        21.04        41.42         9.01        35.34        32.32 
TCGA-68-8250 TCGA-90-7766 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK 
        8.02         9.50         0.16        18.38        16.14        19.36 
TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 
        5.69         0.07        76.80        39.85        65.65        16.80 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
        8.58        75.75       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 
       36.07         2.79       154.32       119.54        99.16        70.16 
TCGA-21-1076 TCGA-21-1079 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
       60.89        31.73        43.23        33.93        10.82         7.33 
TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
        4.31        14.10        27.02        20.48        35.08        48.33 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       38.17        13.12        11.77        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 
        0.79        86.30        71.34        11.74        18.84        56.32 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-AAS8 TCGA-33-AASB 
       97.94        79.53       103.53        14.07        36.62         6.94 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2608 TCGA-34-5231 TCGA-34-5236 TCGA-34-5241 
       44.19        27.16        32.88        65.23         9.07        16.93 
TCGA-34-5927 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-37-3789 TCGA-37-3792 
       44.75         1.12         4.04        26.43         0.43         0.39 
TCGA-37-4130 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 
        8.12         6.81         3.39        37.58        21.70       126.58 
TCGA-39-5019 TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
      111.35       102.18        24.33        60.53        36.39        71.18 
TCGA-39-5037 TCGA-43-2576 TCGA-43-3920 TCGA-43-6771 TCGA-43-7656 TCGA-43-8116 
       55.56        40.21        33.11         5.46        19.59        11.77 
TCGA-46-3766 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 
       12.16         9.83         4.44        10.65        13.91         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 
       29.95        28.34         5.46        30.35        28.96        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       18.25        21.90        18.48        14.53        31.27        30.41 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
       19.76         6.51        17.49        33.24        14.96         4.93 
TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A62T 
        1.35        15.81        20.94        19.23        13.32        14.47 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-A46K 
        0.03        13.25        13.55        29.95        16.47        34.36 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 TCGA-60-2708 TCGA-60-2719 TCGA-60-2722 
       10.22        96.82        21.93        80.45        42.64        29.85 
TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
       35.90        26.83        11.77        52.67        70.13        70.42 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP 
       55.30       102.67        59.97        45.57        11.34        25.28 
TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 
       78.28        36.16        53.88        34.59        43.10        21.07 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        1.02         2.01         0.92        43.99        21.01        25.05 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 
        2.01         1.02        19.00         2.01        12.03         3.98 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 
       12.00         1.97        25.97        40.01        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       30.02        10.06         4.01        49.05         2.73         6.64 
TCGA-68-8251 TCGA-70-6723 TCGA-77-6842 TCGA-77-7141 TCGA-77-7335 TCGA-77-7463 
       13.35        12.33        29.56         0.49        70.13        46.78 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8136 TCGA-77-8145 TCGA-77-8148 
       32.55        86.76        55.73        39.09         6.97        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
       54.41        65.49        60.53        36.36       150.25        22.29 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
       27.62        38.86        40.24         6.41        36.53        31.30 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
        1.15        25.15        19.04        31.56        26.79        34.52 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
        0.76        22.45        16.77         5.29        32.71         2.01 
TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC 
        7.76        18.08        22.59        30.28        34.13        19.86 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 
       19.73        16.21        15.85        14.96        12.39         3.65 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-8491 
       11.77        20.22        22.62         3.48         5.26        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       14.14        17.69        30.81        30.67        21.34        27.16 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HH 
       18.58        20.71        12.89        13.18        11.84         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX 
       13.74         4.21        25.32        14.73        83.57         3.65 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
        3.72        12.72        43.89 

$`21Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-21-A5DI 
       12.20         4.47       123.19         4.80        27.19        32.19 
TCGA-22-1000 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-6737 TCGA-34-2605 
       14.93        64.93        22.06       133.74        19.76        28.96 
TCGA-34-2609 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 
       31.27         7.76        78.18        11.61        19.99        13.05 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2696 TCGA-63-A5MH 
       17.00        16.77        17.85         0.13         3.58        66.61 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-96-7545 
       20.78        42.08        30.81        14.07        21.04        57.07 
TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3419 
        2.76        21.21        19.10        40.90         0.43        92.42 
TCGA-18-3421 TCGA-18-5592 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 
       86.96        49.94        46.88        34.78        15.58       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 
        9.34       119.80        31.63        88.11        41.69        21.99 
TCGA-22-1005 TCGA-22-1011 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4605 
       64.21         1.74        24.13         0.56        34.75        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 
       19.30         9.57        79.20        30.12        62.86        16.64 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
      173.82       151.27        54.44        63.35         4.70         0.30 
TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-5232 TCGA-34-5234 
      110.99       118.36         2.63        61.61        81.24        74.66 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-A5IX 
       60.30        50.66        39.32         4.96        38.79        33.90 
TCGA-37-3783 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-39-5011 
        4.01         7.96         7.46         7.82         0.39       133.25 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5035 
       68.58        55.20        82.52         1.71         1.94        68.38 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       17.06        38.66        39.12        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-6773 TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
       21.47         3.81        13.38         9.73        14.20        13.32 
TCGA-46-3767 TCGA-51-4079 TCGA-52-7811 TCGA-52-7812 TCGA-56-7731 TCGA-56-8304 
       13.02         0.39         8.75        27.45         0.10         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       26.89        14.07         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8391 TCGA-58-8393 
        9.93        20.25        18.74         0.26        71.24        34.78 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       85.12        56.65        35.24        29.92        21.11        12.23 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       37.94        92.71        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2724 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI 
       48.49         3.19        23.57        68.15        70.62        58.65 
TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MT TCGA-66-2727 TCGA-66-2737 TCGA-66-2744 
       14.99        89.29        16.37        16.96         2.01         0.99 
TCGA-66-2756 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
        0.99         0.99         2.01         2.01         7.07        23.01 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2783 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 
        3.02        19.00        24.95         4.04        22.98        54.08 
TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 
        6.94        16.18        14.73        12.07        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 
       23.28        11.18       140.09        73.22       106.95         0.16 
TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
        6.51        37.81       156.66        12.59        53.92        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-A5FZ TCGA-77-A5G1 
      104.09        11.54        26.40        27.39       126.18       132.36 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-7699 
        5.92        61.94         9.67        41.39        34.95        32.91 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8072 TCGA-85-8277 
        1.38        29.95        18.94        24.13        30.64        10.09 
TCGA-85-8288 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
       13.22         3.09        15.39        36.59        38.14        12.59 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A512 TCGA-85-A513 
       30.97        24.36        30.48        27.16        15.29        29.92 
TCGA-90-6837 TCGA-90-7767 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 
       24.92         2.93        10.59         2.70         4.01         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
        4.01         5.03        71.01        18.31        17.46        27.68 
TCGA-98-7454 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-L3-A524 
       21.44        18.15         2.01        27.02        20.32        16.11 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN 
       13.41         4.54        64.54        57.30         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HT TCGA-O2-A52N TCGA-O2-A5IB TCGA-XC-AA0X 
       43.92        26.43        33.07        11.18         0.20 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.03               0.10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            154.32             173.82 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             21.07              22.75 
[1] "0.0 - 154.3 (21.1)" "0.1 - 173.8 (22.8)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         1       49       81        2        40        43
  21Q LOSS WILD-TYPE       1       40       71        0        25        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  21Q LOSS MUTATED           2         29          8        6
  21Q LOSS WILD-TYPE         1         34         11        1
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 49                 40
  STAGE IB                 81                 71
  STAGE II                  2                  0
  STAGE IIA                40                 25
  STAGE IIB                43                 52
  STAGE III                 2                  1
  STAGE IIIA               29                 34
  STAGE IIIB                8                 11
  STAGE IV                  6                  1
[1] 10  2
[1] 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    59 160  33  12
  21Q LOSS WILD-TYPE  53 134  38  12
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               59                 53
  T2              160                134
  T3               33                 38
  T4               12                 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   170  70  20   1
  21Q LOSS WILD-TYPE 147  63  20   4
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0              170                147
  N1               70                 63
  N2               20                 20
  N3                1                  4
[1] 4 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   223   6
  21Q LOSS WILD-TYPE 188   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    223    6
  21Q LOSS WILD-TYPE  188    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              223                188
  1                6                  1
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    51 213
  21Q LOSS WILD-TYPE  79 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     51  213
  21Q LOSS WILD-TYPE   79  158
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               51                 79
  MALE                213                158
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   201  31
  21Q LOSS WILD-TYPE 183  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    201   31
  21Q LOSS WILD-TYPE  183   22
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO               201                183
  YES               31                 22
[1] 2 2
[1] FALSE
D79V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                       7
  21Q LOSS WILD-TYPE                                     8
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  21Q LOSS MUTATED                                        2
  21Q LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                         0
  21Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                           255
  21Q LOSS WILD-TYPE                                                         224
D79V10, multiclass
                                                             clus
vv                                                            21Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              255
                                                             clus
vv                                                            21Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                224
[1] 4 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   209   6   2  10
  21Q LOSS WILD-TYPE 190   6   2  13
D79V13, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              209                190
  R1                6                  6
  R2                2                  2
  RX               10                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       3                        14   184
  21Q LOSS WILD-TYPE     6                        17   165
D79V14, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN               14                 17
  WHITE                                  184                165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V15, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     6 162
  21Q LOSS WILD-TYPE   2 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6  162
  21Q LOSS WILD-TYPE    2  155
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO              162                155
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    51  46
  22Q LOSS WILD-TYPE 229 168
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                97                397 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                46                168 
$`22Q LOSS MUTATED`
TCGA-18-3407 TCGA-18-4083 TCGA-21-A5DI TCGA-33-6737 TCGA-43-2578 TCGA-43-7658 
        4.47         6.18        32.19        19.76        22.49        78.18 
TCGA-68-8250 TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W 
        8.02        76.80        39.85        65.65        16.80         8.58 
TCGA-18-3417 TCGA-21-1070 TCGA-21-1071 TCGA-21-1080 TCGA-21-5783 TCGA-21-5787 
       36.07       119.54        46.88       122.43        88.11        10.82 
TCGA-22-0940 TCGA-22-1016 TCGA-22-4594 TCGA-22-5480 TCGA-22-5483 TCGA-33-4582 
       21.99        27.02        48.33        71.34        18.84       103.53 
TCGA-33-4583 TCGA-33-4587 TCGA-33-AAS8 TCGA-33-AASB TCGA-34-5928 TCGA-37-3792 
      151.27        54.44        36.62         6.94        39.32         0.39 
TCGA-37-4129 TCGA-37-4132 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 
        7.96         7.46         3.39        37.58       133.25       126.58 
TCGA-39-5029 TCGA-39-5040 TCGA-43-2581 TCGA-43-6771 TCGA-46-3769 TCGA-52-7812 
       24.33        17.06        38.66         5.46         4.44        27.45 
TCGA-56-7222 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-A62T TCGA-60-2695 
       18.48         3.48        26.89        14.07        14.47        21.11 
TCGA-63-6202 TCGA-63-A5MJ TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MY TCGA-66-2727 
       52.67        59.97        11.34        25.28        34.59        16.96 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2759 TCGA-66-2766 TCGA-66-2771 
        1.02         2.01        43.99        25.05         1.02        19.00 
TCGA-66-2778 TCGA-66-2782 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 
       19.00        12.00         4.04        22.98         5.03        10.06 
TCGA-68-A59I TCGA-70-6723 TCGA-77-7138 TCGA-77-7337 TCGA-77-7465 TCGA-77-8139 
       16.18        12.33        11.18       106.95        32.55       104.09 
TCGA-77-8150 TCGA-77-A5G6 TCGA-85-6560 TCGA-85-7697 TCGA-85-8048 TCGA-85-8049 
       54.41        22.29        41.39        34.95        25.15        19.04 
TCGA-85-8072 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A510 TCGA-85-A53L 
       30.64        12.59        18.08        22.59        15.85        12.39 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-98-7454 
       20.22        22.62        10.59         4.01         2.30        21.44 
TCGA-98-A53B TCGA-MF-A522 TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HQ 
        2.01        11.84        13.74         2.89        43.92        14.73 
TCGA-NK-A5CX 
        3.65 

$`22Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 
       12.20       123.19         4.80        31.99        27.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       48.82        60.66        64.93        22.06       129.01       133.74 
TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 
        1.55        31.50        28.96        31.27        17.88        18.38 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 
        7.76         2.93        11.61        12.03        19.99        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
        3.45        17.00        16.77        17.85        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
        3.58        41.42         9.01        35.34        32.32        66.61 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
       20.78        42.08        30.81         9.50        14.07        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
        0.16        18.38        16.14        57.07        19.36         2.76 
TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HR TCGA-NK-A7XE 
        5.69        21.21        19.10         0.07        40.90         0.43 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 
       75.75       117.57        11.34        23.54        92.15        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 TCGA-21-1075 
       86.96         2.79       154.32        49.94        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
       60.89        34.78        15.58        31.73         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1002 
       43.23        31.63        41.69        33.93         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
       64.21         1.74        14.10        20.48        35.08        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
        0.56        38.17        34.75        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       86.30        79.20        11.74        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-6738 
       16.64        97.94        79.53       173.82        14.07        63.35 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
        4.70         0.30       110.99        44.19       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        2.63        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
        9.07        60.30        50.66        16.93        44.75         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        38.79         4.04        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EN 
        0.43         8.12         7.82         6.81         0.39        21.70 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      111.35        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        60.53        36.39        68.38        71.18        55.56 
TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       40.21        39.12        33.11        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
       21.47         3.81        19.59        13.38        11.77         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 
       14.20        13.32        12.16        13.02         9.83        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       13.91         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
       30.35         8.75        28.96        12.43        18.25        21.90 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       14.53        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8503 TCGA-56-8622 
       17.49        33.24        14.96         4.93         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 
       20.94        19.23        13.32        18.74         0.26         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.25        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 
       85.12        34.36        56.65        35.24        29.92        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       10.22        96.82        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       49.48        66.54        56.91        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
        3.19        29.85        35.90        23.57        26.83        11.77 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG 
       70.13        70.42        68.15        55.30       102.67        70.62 
TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       58.65        45.57        14.99        89.29        78.28        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       36.16        53.88        43.10         2.01        21.07         0.99 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
        0.92         0.99        21.01         0.99         2.01         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 
        2.01         7.07        23.01         3.02         2.01        12.03 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        3.98        24.95         1.97        25.97        40.01        22.98 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       30.02        54.08         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 
        6.94        13.35        14.73        12.07        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       75.09        23.28       140.09         0.49        73.22        70.13 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
        0.16        46.78         6.51        86.76        55.73        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 
      156.66        12.59        53.92        39.09        17.72        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 
       26.40        27.39         6.97        66.51        65.49        60.53 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
       36.36       126.18       132.36       150.25         5.92        61.94 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86         9.67        40.24         6.41        36.53 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
       31.30        32.91         1.38         1.15        29.95        18.94 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       24.13        31.56        26.79        34.52        10.09         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       13.22        22.45        16.77         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL 
        2.01        15.39         7.76        36.59        38.14        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       34.13        30.97        19.86        24.36        30.48        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 
       27.16        16.21        14.96        15.29        29.92         3.65 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
       24.92         2.93        11.77         2.70         3.48         5.26 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        26.63        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       18.31        17.46        27.68        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
       27.16        18.15        27.02        20.32        18.58        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG 
       12.89        16.11        13.18        13.41         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HT 
        1.22        57.30         4.21        49.28        25.32        26.43 
TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       83.57        33.07         3.72        12.72        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.39               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            151.27             173.82 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             20.22              22.06 
[1] "0.4 - 151.3 (20.2)" "0.0 - 173.8 (22.1)"
[1] "hr=" "1.1"
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         1       17       21        0        16        18
  22Q LOSS WILD-TYPE       1       72      131        2        49        77
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  22Q LOSS MUTATED           0         17          4        2
  22Q LOSS WILD-TYPE         3         46         15        5
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 17                 72
  STAGE IB                 21                131
  STAGE II                  0                  2
  STAGE IIA                16                 49
  STAGE IIB                18                 77
  STAGE III                 0                  3
  STAGE IIIA               17                 46
  STAGE IIIB                4                 15
  STAGE IV                  2                  5
[1] 10  2
[1] 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    22  58  16   2
  22Q LOSS WILD-TYPE  90 236  55  22
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               22                 90
  T2               58                236
  T3               16                 55
  T4                2                 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                  N0  N1  N2  N3
  22Q LOSS MUTATED    57  25  13   3
  22Q LOSS WILD-TYPE 260 108  27   2
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               57                260
  N1               25                108
  N2               13                 27
  N3                3                  2
[1] 4 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    79   2
  22Q LOSS WILD-TYPE 332   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     79    2
  22Q LOSS WILD-TYPE  332    5
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               79                332
  1                2                  5
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    24  74
  22Q LOSS WILD-TYPE 106 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24   74
  22Q LOSS WILD-TYPE  106  297
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               24                106
  MALE                 74                297
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    66  18
  22Q LOSS WILD-TYPE 318  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     66   18
  22Q LOSS WILD-TYPE  318   35
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                66                318
  YES               18                 35
[1] 2 2
[1] FALSE
D80V9, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED                                       3
  22Q LOSS WILD-TYPE                                    12
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  22Q LOSS MUTATED                                        2
  22Q LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED                                         1
  22Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                            92
  22Q LOSS WILD-TYPE                                                         387
D80V10, multiclass
                                                             clus
vv                                                            22Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               92
                                                             clus
vv                                                            22Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                387
[1] 4 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    73   4   1   4
  22Q LOSS WILD-TYPE 326   8   3  19
D80V13, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               73                326
  R1                4                  8
  R2                1                  3
  RX                4                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       3                         8    63
  22Q LOSS WILD-TYPE     6                        23   286
D80V14, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                8                 23
  WHITE                                   63                286
[1] 3 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     2  57
  22Q LOSS WILD-TYPE   6 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   57
  22Q LOSS WILD-TYPE    6  260
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               57                260
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    75  68
  XP LOSS WILD-TYPE 205 146
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              143               351 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               68               146 
$`XP LOSS MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-5595 TCGA-22-A5C4 TCGA-34-2605 TCGA-34-2609 
        4.47        31.99        27.19        22.06        28.96        31.27 
TCGA-43-5668 TCGA-43-8118 TCGA-56-7221 TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       18.38         2.93        19.99         0.13         3.58        41.42 
TCGA-60-2712 TCGA-60-2721 TCGA-77-A5GA TCGA-90-7766 TCGA-98-8020 TCGA-NK-A5CT 
        9.01        32.32        42.08         9.50         2.76        65.65 
TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3412 TCGA-18-3417 TCGA-18-4086 TCGA-18-5592 
       16.80        75.75        11.34        36.07         2.79        49.94 
TCGA-21-1072 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 TCGA-22-4591 
       99.16       122.43       119.80        43.23        21.99        20.48 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
       19.30        11.77        63.55        44.25        71.34        79.20 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-33-4566 TCGA-33-4582 TCGA-33-A5GW 
       18.84        30.12        56.32       173.82       103.53         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-5927 TCGA-34-5929 
       36.62       110.99       118.36        27.16        44.75         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL 
        1.12        38.79        26.43         6.81         0.39        37.58 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5028 TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 
       68.58       102.18         1.71        21.47        19.59        11.77 
TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 
        4.44        10.65         0.39         0.39        29.95        30.35 
TCGA-56-7222 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8624 TCGA-56-8625 
       18.48        33.24        14.96         4.93        13.81        10.36 
TCGA-56-8629 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-60-2707 
       15.81        13.55        29.95        71.24        16.47        21.93 
TCGA-60-2710 TCGA-60-2713 TCGA-63-7023 TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MT 
       66.54        56.91        55.30        58.65        25.28        16.37 
TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 TCGA-66-2757 TCGA-66-2768 
       36.16        34.59        16.96         1.02        43.99         2.01 
TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2789 
        3.02        12.03         3.98        12.00        25.97         4.04 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       22.98        30.02         4.01        49.05         2.73         6.64 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7142 TCGA-77-8009 TCGA-77-8140 
       12.33        29.56        23.28        73.22        55.73        11.54 
TCGA-77-8144 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 
       27.39        60.53       150.25        27.62         9.67        40.24 
TCGA-85-7698 TCGA-85-7699 TCGA-85-8071 TCGA-85-8288 TCGA-85-8352 TCGA-85-8354 
       31.30        32.91        26.79        13.22         5.29        32.71 
TCGA-85-8479 TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M TCGA-85-A512 
       15.39        36.59        34.13        19.73        27.16        15.29 
TCGA-92-8063 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 
        4.01         4.01         5.03        26.63        17.69        71.01 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HG 
       18.15         2.01        20.71        13.18         4.54        64.54 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HO TCGA-O2-A52S TCGA-O2-A5IB 
       57.30         2.89        43.92        12.72        11.18 

$`XP LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1000 
       12.20       123.19         4.80         6.18        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 
       48.82        60.66        64.93       129.01       133.74         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-39-5039 TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 
       19.76        31.50        17.88        22.49         7.76        78.18 
TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       11.61        12.03        13.05         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
       17.85        21.04        35.34        66.61         8.02        20.78 
TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
       30.81        14.07        21.04         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       57.07        19.36         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 
       76.80        39.85        40.90         0.43         8.58       117.57 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 
       23.54        92.15        92.42        86.96       154.32       119.54 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       46.88        70.16        60.89        34.78        15.58        31.73 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        9.34        31.63        88.11        41.69        33.93        10.82 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        7.33         4.31        64.21         1.74        14.10        27.02 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       35.08        48.33        24.13         0.56        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 
       13.12        32.02         9.57        14.63         0.79        86.30 
TCGA-22-5482 TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 
       11.74        62.86        16.64        97.94        79.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASI 
       14.07        54.44        63.35         4.70         6.94        44.19 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        2.63        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-8455 
        9.07        60.30        50.66        16.93        39.32         4.04 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       33.90         4.01         0.43         0.39         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 
        7.46         7.82         3.39        21.70       133.25       126.58 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
      111.35        55.20        82.52        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       36.39        68.38        71.18        55.56        17.06        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       38.66        39.12        33.11        27.91        22.98        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
        5.46         3.81        13.38         9.73        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6026 TCGA-52-7622 TCGA-52-7809 
       12.16        13.02         9.83        13.91        28.34         5.46 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        8.75        27.45        28.96        12.43        18.25        21.90 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       14.53        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
       17.49         3.48        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
       22.75         9.93        20.25        20.94        19.23        13.32 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8393 
       18.74         0.26        14.47         0.03        13.25        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       85.12        34.36        56.65        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 
       12.23        10.22        96.82        37.94        92.71        80.45 
TCGA-60-2709 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       49.48        50.33        48.49        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
       35.90        23.57        26.83        11.77        52.67        70.13 
TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML 
       70.42        68.15       102.67        70.62        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MW TCGA-66-2734 
       14.99        11.34        89.29        78.28        53.88        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
        2.01        21.07         0.99         2.01         0.92         0.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 
        7.07        23.01        19.00         2.01        19.00        24.95 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 
        1.97        40.01        22.98         5.03        10.06        54.08 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 
        6.94        13.35        16.18        14.73        12.07        73.12 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       75.09        11.18       140.09         0.49        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
        0.16        46.78        32.55         6.51        86.76        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
      156.66        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
       26.40         6.97        66.51        54.41        65.49        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH 
      126.18       132.36        22.29         5.92        61.94        38.86 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 
       41.39         6.41        36.53        34.95         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       29.95        18.94        25.15        19.04        24.13        31.56 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 
       30.64        34.52        10.09         0.76        22.45        16.77 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        3.09         2.01         7.76        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       22.59        30.28        30.97        19.86        24.36        30.48 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96        29.92        12.39         3.65 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       24.92         2.93        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-A4VJ TCGA-96-8169 
        2.70         3.48         5.26         2.30        14.14        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        27.68        21.44        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 
       27.16        27.02        20.32        18.58        12.89        16.11 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN 
       13.41        11.84         1.22        13.74         4.21        49.28 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       25.32        14.73        26.43        83.57         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
        3.72        43.89         0.20 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.13              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           173.82            156.66 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            22.06             21.34 
[1] "0.1 - 173.8 (22.1)" "0.0 - 156.7 (21.3)"
[1] "hr=" "1.2"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         0       25       42        1        24        28
  XP LOSS WILD-TYPE       2       64      110        1        41        67
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  XP LOSS MUTATED           2         14          6        1
  XP LOSS WILD-TYPE         1         49         13        6
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                25                64
  STAGE IB                42               110
  STAGE II                 1                 1
  STAGE IIA               24                41
  STAGE IIB               28                67
  STAGE III                2                 1
  STAGE IIIA              14                49
  STAGE IIIB               6                13
  STAGE IV                 1                 6
[1] 10  2
[1] 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    37  78  20  10
  XP LOSS WILD-TYPE  75 216  51  14
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              37                75
  T2              78               216
  T3              20                51
  T4              10                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 LOSS MUTATED    92  44   7   1
  XP LOSS WILD-TYPE 225  89  33   4
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              92               225
  N1              44                89
  N2               7                33
  N3               1                 4
[1] 4 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   120   1
  XP LOSS WILD-TYPE 291   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    120    1
  XP LOSS WILD-TYPE  291    6
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0             120               291
  1               1                 6
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    40 105
  XP LOSS WILD-TYPE  90 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     40  105
  XP LOSS WILD-TYPE   90  266
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              40                90
  MALE               105               266
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   110  16
  XP LOSS WILD-TYPE 274  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    110   16
  XP LOSS WILD-TYPE  274   37
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO              110               274
  YES              16                37
[1] 2 2
[1] FALSE
D81V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  XP LOSS MUTATED                                       4
  XP LOSS WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  XP LOSS MUTATED                                        2
  XP LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  XP LOSS MUTATED                                         0
  XP LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XP LOSS MUTATED                                                           139
  XP LOSS WILD-TYPE                                                         340
D81V10, multiclass
                                                             clus
vv                                                            XP LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             139
                                                             clus
vv                                                            XP LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D81V11, continuous
D81V12, continuous
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED   115   1   0   8
  XP LOSS WILD-TYPE 284  11   4  15
D81V13, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0             115               284
  R1               1                11
  R2               0                 4
  RX               8                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       3                        11    96
  XP LOSS WILD-TYPE     6                        20   253
D81V14, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              11                20
  WHITE                                  96               253
[1] 3 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     1  91
  XP LOSS WILD-TYPE   7 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1   91
  XP LOSS WILD-TYPE    7  226
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              91               226
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    58  55
  XQ LOSS WILD-TYPE 222 159
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              113               381 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               55               159 
$`XQ LOSS MUTATED`
TCGA-18-3416 TCGA-18-5595 TCGA-22-A5C4 TCGA-33-4533 TCGA-34-2605 TCGA-43-5668 
       31.99        27.19        22.06       133.74        28.96        18.38 
TCGA-56-7221 TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 TCGA-60-2721 TCGA-90-7766 
       19.99         0.13         3.58         9.01        32.32         9.50 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-4086 TCGA-18-5592 TCGA-21-1072 TCGA-21-1080 
       65.65        16.80         2.79        49.94        99.16       122.43 
TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 TCGA-22-4591 TCGA-22-4607 TCGA-22-4613 
      119.80        43.23        21.99        20.48        19.30        11.77 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5481 TCGA-22-5485 TCGA-22-5491 TCGA-33-4582 
       63.55        44.25        79.20        30.12        56.32       103.53 
TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI 
       54.44         4.70         0.30        36.62       110.99        44.19 
TCGA-33-AASL TCGA-34-2600 TCGA-34-5927 TCGA-34-5929 TCGA-37-4135 TCGA-37-4141 
       27.16        61.61        44.75         4.96         6.81         0.39 
TCGA-37-A5EL TCGA-39-5027 TCGA-39-5028 TCGA-43-7656 TCGA-43-8116 TCGA-46-3769 
       37.58       102.18         1.71        19.59        11.77         4.44 
TCGA-46-6025 TCGA-51-4080 TCGA-52-7810 TCGA-56-7222 TCGA-56-7823 TCGA-56-8083 
       10.65         0.39        30.35        18.48        33.24         4.93 
TCGA-56-8625 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-60-2713 
       10.36        13.55        29.95        71.24        16.47        56.91 
TCGA-60-2726 TCGA-63-7023 TCGA-63-A5MI TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       11.77        55.30        58.65        53.88        34.59        16.96 
TCGA-66-2753 TCGA-66-2757 TCGA-66-2768 TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 
        1.02        43.99         2.01        12.03        12.00        25.97 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
        4.04        22.98        30.02         4.01         2.73         6.64 
TCGA-77-6845 TCGA-77-7142 TCGA-77-8136 TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 
       23.28        73.22        39.09        11.54        27.39        65.49 
TCGA-77-8154 TCGA-77-A5G3 TCGA-85-6175 TCGA-85-7699 TCGA-85-8071 TCGA-85-8288 
       60.53       150.25         9.67        32.91        26.79        13.22 
TCGA-85-8352 TCGA-85-8479 TCGA-85-8580 TCGA-85-A4QR TCGA-85-A512 TCGA-92-8063 
        5.29        15.39        36.59        19.73        15.29         4.01 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-98-8022 TCGA-98-A53A 
        4.01         5.03        26.63        71.01        30.67        18.15 
TCGA-98-A53B TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
        2.01        13.18         4.54        64.54         1.22        57.30 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-O2-A52S TCGA-O2-A5IB 
        4.21         2.89        43.92        12.72        11.18 

$`XQ LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI 
       12.20         4.47       123.19         4.80         6.18        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4589 
       14.93        48.82        60.66        64.93       129.01         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-7657 
       19.76        31.50        31.27        17.88        22.49         7.76 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 
       78.18         2.93        11.61        12.03        13.05         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2711 TCGA-60-2715 
       17.00        16.77        17.85        21.04        41.42        35.34 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 
       66.61         8.02        20.78        42.08        30.81        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       21.04         0.16        18.38        16.14        57.07        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE 
        2.76         5.69        21.21        19.10         0.07        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       39.85        40.90         0.43         8.58        75.75       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       11.34        23.54        92.15        36.07        92.42        86.96 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      154.32       119.54        46.88        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
       15.58        31.73         9.34        31.63        88.11        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       33.93        10.82         7.33         4.31        64.21         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       14.10        27.02        35.08        48.33        24.13         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-5474 
       38.17        34.75        13.12        32.02         9.57        14.63 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 
        0.79        86.30        71.34        11.74        18.84        62.86 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
       16.64        97.94        79.53       173.82       151.27        14.07 
TCGA-33-6738 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 
       63.35         6.94       118.36         2.63        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       81.24        74.66         9.07        60.30        50.66        16.93 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       39.32         1.12        38.79         4.04        26.43        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        4.01         0.43         0.39         7.96         8.12         7.46 
TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        7.82         3.39        21.70       133.25       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       68.58        55.20        82.52        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       36.39        68.38        71.18        55.56        17.06        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       38.66        39.12        33.11        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U 
       21.47         5.46         3.81        13.38         9.73        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 
       13.32        12.16        13.02         9.83        13.91         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
       29.95        28.34         5.46         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       12.43        18.25        21.90        14.53        31.27        30.41 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8304 
       19.76         6.51         0.10        17.49        14.96         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       26.89        14.07         1.35         1.81        22.75        13.81 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
        9.93        20.25        15.81        20.94        19.23        13.32 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8393 
       18.74         0.26        14.47         0.03        13.25        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       85.12        34.36        56.65        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       12.23        10.22        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       80.45        49.48        66.54        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 
        3.19        29.85        35.90        23.57        26.83        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ 
       70.13        70.42        68.15       102.67        70.62        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       45.57        14.99        11.34        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       16.37        36.16        43.10         2.01        21.07         0.99 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        2.01         0.92         0.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
        2.01         1.02         2.01         7.07        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 
        3.02         2.01        19.00         3.98        24.95         1.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
       40.01        22.98         5.03        10.06        54.08        49.05 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 
        6.94        13.35        16.18        14.73        12.07        12.33 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       29.56        73.12        75.09        11.18       140.09         0.49 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       70.13       106.95         0.16        46.78        32.55         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       86.76        55.73        37.81       156.66        12.59        53.92 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       17.72       104.09        26.40         6.97        66.51        54.41 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       36.36       126.18       132.36        22.29         5.92        61.94 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86        41.39        40.24         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
       34.95        31.30         1.38         1.15        29.95        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 
       25.15        19.04        24.13        31.56        30.64        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
       10.09         0.76        22.45        16.77         3.09        32.71 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        2.01         7.76        38.14        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       30.28        34.13        30.97        19.86        24.36        30.48 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       27.16        16.21        15.85        14.96        29.92        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
        3.65        24.92         2.93        11.77        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-A4VJ 
       10.59         2.70         3.48         5.26         2.30        14.14 
TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       17.69        18.31        17.46        27.68        21.44        30.81 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
       21.34        27.16        27.02        20.32        18.58        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HJ TCGA-NC-A5HN 
       12.89        16.11        13.41        11.84        13.74        49.28 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       25.32        14.73        26.43        83.57         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
        3.72        43.89         0.20 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.13              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           150.25            173.82 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            21.99             21.70 
[1] "0.1 - 150.2 (22.0)" "0.0 - 173.8 (21.7)"
[1] "hr=" "1.2"
D82V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         0       25       31        0        16        21
  XQ LOSS WILD-TYPE       2       64      121        2        49        74
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  XQ LOSS MUTATED           2         12          5        0
  XQ LOSS WILD-TYPE         1         51         14        7
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                25                64
  STAGE IB                31               121
  STAGE II                 0                 2
  STAGE IIA               16                49
  STAGE IIB               21                74
  STAGE III                2                 1
  STAGE IIIA              12                51
  STAGE IIIB               5                14
  STAGE IV                 0                 7
[1] 10  2
[1] 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    35  54  16   9
  XQ LOSS WILD-TYPE  77 240  55  15
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              35                77
  T2              54               240
  T3              16                55
  T4               9                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
  XQ LOSS MUTATED    73  34   6   1
  XQ LOSS WILD-TYPE 244  99  34   4
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              73               244
  N1              34                99
  N2               6                34
  N3               1                 4
[1] 4 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    93   0
  XQ LOSS WILD-TYPE 318   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     93    0
  XQ LOSS WILD-TYPE  318    7
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              93               318
  1               0                 7
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    34  80
  XQ LOSS WILD-TYPE  96 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     34   80
  XQ LOSS WILD-TYPE   96  291
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              34                96
  MALE                80               291
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    86  13
  XQ LOSS WILD-TYPE 298  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     86   13
  XQ LOSS WILD-TYPE  298   40
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               86               298
  YES              13                40
[1] 2 2
[1] FALSE
D82V9, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED                                       5
  XQ LOSS WILD-TYPE                                    10
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  XQ LOSS MUTATED                                        1
  XQ LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED                                         1
  XQ LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                           107
  XQ LOSS WILD-TYPE                                                         372
D82V10, multiclass
                                                             clus
vv                                                            XQ LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             107
                                                             clus
vv                                                            XQ LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               372
[1] 4 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    91   1   0   4
  XQ LOSS WILD-TYPE 308  11   4  19
D82V13, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              91               308
  R1               1                11
  R2               0                 4
  RX               4                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       0                         8    80
  XQ LOSS WILD-TYPE     9                        23   269
D82V14, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               8                23
  WHITE                                  80               269
[1] 3 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     0  69
  XQ LOSS WILD-TYPE   8 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   69
  XQ LOSS WILD-TYPE    8  248
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              69               248
[1] 2 2
[1] FALSE
