[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/15084586/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/15093662/transformed.cor.cli.txt"

nPatients in clinical file=495, in cluster file=501, common to both=493
[1]  82 493
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               89               404 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               89               404 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              200               293 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              200               293 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              218               275 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              218               275 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              138               355 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              138               355 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              105               388 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              105               388 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              311               182 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              311               182 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               32               461 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               32               461 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               23               470 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               23               470 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              305               188 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              305               188 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               92               401 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               92               401 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              108               385 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              108               385 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               92               401 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               92               401 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              238               255 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              238               255 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              218               275 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              218               275 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              128               365 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              128               365 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              255               238 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              255               238 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               61               432 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               61               432 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               91               402 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               91               402 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                78                415 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                78                415 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                44                449 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                44                449 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                73                420 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                73                420 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                90                403 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                90                403 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               225                268 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               225                268 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               150                343 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               150                343 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                35                458 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                35                458 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               128                365 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               128                365 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               103                390 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               103                390 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                82                411 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                82                411 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                83                410 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                83                410 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                66                427 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                66                427 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               154                339 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               154                339 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               149                344 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               149                344 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               104                389 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               104                389 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               110                383 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               110                383 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               157                336 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               157                336 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               256                237 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               256                237 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               245                248 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               245                248 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                56                437 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                56                437 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               216                277 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               216                277 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               65               428 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               65               428 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               82               411 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               82               411 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              147               346 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              147               346 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               59               434 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               59               434 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               20               473 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               20               473 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               40               453 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               40               453 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              307               186 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              307               186 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               69               424 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               69               424 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              310               183 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              310               183 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              292               201 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              292               201 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               75               418 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               75               418 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              285               208 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              285               208 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              112               381 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              112               381 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              113               380 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              113               380 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               57               436 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               57               436 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               50               443 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               50               443 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              239               254 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              239               254 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               47               446 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               47               446 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              304               189 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              304               189 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              241               252 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              241               252 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               210                283 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               210                283 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               224                269 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               224                269 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               170                323 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               170                323 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               140                353 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               140                353 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                38                455 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                38                455 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                47                446 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                47                446 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               308                185 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               308                185 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               161                332 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               161                332 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               140                353 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               140                353 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               160                333 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               160                333 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               179                314 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               179                314 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               288                205 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               288                205 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                94                399 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                94                399 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               139                354 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               139                354 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               187                306 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               187                306 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               161                332 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               161                332 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               107                386 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               107                386 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                451 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                451 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                46                447 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                46                447 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               259                234 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               259                234 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                97                396 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                97                396 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              141               352 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              141               352 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              109               384 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              109               384 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "COMPLETENESS_OF_RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCH_NUMBER"                          

Input Data has 23 rows and 493 columns.

[1] "Batch" "23"   
[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=188,	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=324,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	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:'DCC_UPLOAD_DATE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=109,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=106,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH_NUMBER':	nDistinctValues=36,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "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 493 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY_PERFORMANCE_SCORE"           
 [8] "HISTOLOGICAL_TYPE"                     
 [9] "RADIATIONS_RADIATION_REGIMENINDICATION"
[10] "NUMBER_PACK_YEARS_SMOKED"              
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[12] "COMPLETENESS_OF_RESECTION"             
[13] "RACE"                                  
[14] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=45, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
111 290  69  23 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
111 290  69  23 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
111 290  69  23 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
111 290  69  23 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
312 131  39   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
312 131  39   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
312 131  39   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
312 131  39   5 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=5, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=106, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=55, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, 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  31
  1P GAIN WILD-TYPE 226 165
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               86               391 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               31               165 
$`1P GAIN MUTATED`
TCGA-18-3414 TCGA-21-1070 TCGA-21-1081 TCGA-21-1082 TCGA-21-5787 TCGA-22-1011 
       23.54       119.54         9.34       119.80        10.82         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-5481 TCGA-22-5483 TCGA-33-4533 TCGA-33-4582 
       14.10        27.02        79.20        18.84       133.74       103.53 
TCGA-33-6738 TCGA-34-2608 TCGA-34-5231 TCGA-34-5240 TCGA-34-7107 TCGA-34-8455 
       27.02        32.88        65.23        12.00         1.12         4.04 
TCGA-34-A5IX TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4141 TCGA-39-5021 
       20.91         0.39         8.12         7.46         0.39        68.58 
TCGA-39-5022 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 TCGA-43-3920 
       55.20        15.58        35.70        17.06        22.49        33.11 
TCGA-43-6143 TCGA-43-6770 TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 TCGA-56-8504 
       12.36        21.47        10.65         5.46        30.35        16.77 
TCGA-58-A46K TCGA-58-A46N TCGA-60-2695 TCGA-60-2708 TCGA-60-2719 TCGA-60-2722 
       34.36        29.92        21.11        80.45        42.64        29.85 
TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MH TCGA-63-A5MS TCGA-63-A5MW 
       35.90        26.83        11.77        66.61        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-77-7140 
       12.00        24.95        13.35        16.18        11.18        20.78 
TCGA-77-7141 TCGA-77-7338 TCGA-77-8145 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH 
        0.49         0.16         6.97        42.41        30.81        38.86 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7699 TCGA-85-7844 TCGA-85-8072 TCGA-85-A4CL 
       11.97         6.41        32.91        29.95        16.87        25.68 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M TCGA-90-7964 TCGA-90-A4ED TCGA-92-8064 
       14.96        18.18        12.56        14.07        20.22         5.26 
TCGA-94-7557 TCGA-96-8169 TCGA-98-A538 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HG 
        0.16        18.31        27.16        19.10         0.07        51.78 
TCGA-NC-A5HJ TCGA-NC-A5HN 
       13.74        37.22 

$`1P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       11.34        92.15        31.99        36.07         1.64        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
        6.18         2.79       154.32        49.94        27.19        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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       32.19        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       48.82        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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       11.77        31.73        64.93        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
        0.79        54.28        71.34        11.74        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 
       56.32        16.64        22.06         7.63        98.01        79.53 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
      174.08       151.27        14.07        54.44         1.55        19.76 
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-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 
       31.27        67.79        56.38         9.07        23.24        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 
       30.94        18.15         4.96        27.19        26.43         3.95 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 
        0.43         6.58         7.82         6.81         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       74.07        44.75        70.03        60.79         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 
        1.94        27.39        36.39        35.64        17.88        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 
       38.66        27.02        18.38        27.91        24.89         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        3.81        19.59         7.76        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
        2.93        11.61         9.73        14.20        12.03         9.99 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 
       13.91         0.39         0.39        29.95        28.34         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
       27.45        28.96         0.10        18.25         2.04         0.62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
        0.99         0.43         0.99         1.45         1.32         0.85 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 
        6.51         0.10        17.49         3.48        26.89        17.00 
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         1.18        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-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T 
       17.85        21.04        18.74         0.13         0.26         2.76 
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-A46L TCGA-58-A46M TCGA-60-2696 TCGA-60-2697 
       34.78        85.12        56.65        35.24         3.58        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 
       10.22        96.82        37.94        92.71        21.93        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       66.54        41.42         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-63-A5MB TCGA-63-A5MG 
       48.49         3.19        32.32        23.57       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-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 
       89.29        16.37        25.41        36.16        34.59        16.96 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 
        2.01         0.99         1.02         2.01         0.99        43.99 
TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       21.01         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       23.01         3.02         2.01        19.00        12.03         3.98 
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-68-8250 TCGA-68-A59J TCGA-77-6842 
        2.73         6.64         6.94         8.02        14.73        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 
       73.12        75.09        23.28        89.98        42.28        70.13 
TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
      106.95        46.78        15.75         6.51        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       37.81        82.92        12.59        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
      104.09        11.54        26.40        27.39         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       65.49        35.90         0.33       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 
       22.29         5.92        42.08        27.62         9.67        12.99 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 
       36.53        34.95        31.30         1.38         1.15        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
       25.15        19.04        24.13        31.56        14.07        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         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       13.94        12.59         0.10        15.62        19.33        17.72 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       24.36        19.73        16.21        15.85        14.96         0.79 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
       12.39         3.65        24.92         9.50         2.93        11.77 
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-94-7033 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
       21.04        11.70         4.01         5.03        26.63        14.14 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK 
       16.14        17.69        49.87        57.07        17.46        19.36 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       16.57         8.42         2.76        30.81        30.67        21.34 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        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-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK 
       11.84        64.08         4.54         1.22        45.37         4.21 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR 
        2.89        39.85        30.58        24.00        14.73        29.75 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE 
       22.78        83.57        65.49         3.65        16.80         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       33.07         3.72        12.72        43.89         8.58        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            174.08 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             20.5              19.0 
[1] "0.1 - 133.7 (20.5)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         0       10       37        1         9        16
  1P GAIN WILD-TYPE       2       77      114        1        54        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  1P GAIN MUTATED           0         10          2        4
  1P GAIN WILD-TYPE         3         52         19        3
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                10                77
  STAGE IB                37               114
  STAGE II                 1                 1
  STAGE IIA                9                54
  STAGE IIB               16                76
  STAGE III                0                 3
  STAGE IIIA              10                52
  STAGE IIIB               2                19
  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  10   5
  1P GAIN WILD-TYPE  94 233  59  18
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              17                94
  T2              57               233
  T3              10                59
  T4               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                 N0  N1  N2  N3
  1P GAIN MUTATED    62  19   6   1
  1P GAIN WILD-TYPE 250 112  33   4
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              62               250
  N1              19               112
  N2               6                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"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    78   4
  1P GAIN WILD-TYPE 326   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     78    4
  1P GAIN WILD-TYPE  326    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              78               326
  1               4                 3
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    21  68
  1P GAIN WILD-TYPE 106 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     21   68
  1P GAIN WILD-TYPE  106  298
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              21               106
  MALE                68               298
[1] 2 2
[1] FALSE
D1V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                       7
  1P GAIN WILD-TYPE                                     8
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                         0
  1P GAIN WILD-TYPE                                       1
                   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                                                            82
  1P GAIN WILD-TYPE                                                         388
D1V9, multiclass
                                                             clus
vv                                                            1P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     7
  LUNG CLEAR CELL 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)              82
                                                             clus
vv                                                            1P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               388
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2  87
  1P GAIN WILD-TYPE  11 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   87
  1P GAIN WILD-TYPE   11  393
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                2                11
  YES              87               393
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    71   3   1   3
  1P GAIN WILD-TYPE 323   9   3  19
D1V13, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              71               323
  R1               3                 9
  R2               1                 3
  RX               3                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
  1P GAIN MUTATED       2                         6    65
  1P GAIN WILD-TYPE     7                        25   275
D1V14, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               6                25
  WHITE                                  65               275
[1] 3 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  62
  1P GAIN WILD-TYPE   7 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   62
  1P GAIN WILD-TYPE    7  247
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              62               247
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   118  77
  1Q GAIN WILD-TYPE 163 119
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              195               282 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               77               119 
$`1Q GAIN MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
       12.20        75.75       117.57        23.54        92.15        36.07 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 
       49.94       119.54        46.88        99.16        70.16        34.78 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-1011 
        9.34       119.80        41.69        10.82        21.99         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 
       14.10        27.02        48.82        20.48        48.33         0.56 
TCGA-22-4599 TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 
       38.17        19.30        63.55        14.63        54.28        71.34 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4533 
       79.20        18.84        30.12        62.86        22.06       133.74 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       98.01       174.08       103.53       151.27        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 
       27.02         4.70       110.99        44.19         2.63        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 
       32.88        65.23        23.24        12.00        18.15         1.12 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4132 TCGA-37-4133 
        4.04        20.91         3.95         0.39         7.46         7.82 
TCGA-37-4141 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5035 TCGA-39-5037 
        0.39        74.07        68.58        55.20        15.58        35.70 
TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 
       17.06        22.49        38.66        33.11        12.36        21.47 
TCGA-43-7657 TCGA-43-A475 TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 
        7.76         9.73        10.65         0.39        28.34         5.46 
TCGA-52-7810 TCGA-56-7223 TCGA-56-7582 TCGA-56-8504 TCGA-56-8622 TCGA-56-A4BX 
       30.35         0.99         0.85        16.77         1.81        13.32 
TCGA-56-A5DR TCGA-58-8388 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N 
        0.13        13.55        34.78        34.36        35.24        29.92 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2722 TCGA-60-2723 
       21.11        10.22        21.93        80.45        29.85        35.90 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR 
       26.83        11.77        66.61        59.97        45.57        89.29 
TCGA-63-A5MS TCGA-63-A5MU TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       78.28        25.41        53.88        43.10         2.01        21.07 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2770 
        0.92         0.99        21.01        25.05         0.99        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
       19.00         3.02         2.01         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2787 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 
        1.97        40.01        13.35        16.18        14.73        73.12 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7338 
       23.28        11.18        89.98        20.78         0.49         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8145 TCGA-77-8148 
       46.78        15.75        86.76        53.95         6.97         9.63 
TCGA-77-8156 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        0.33        42.41        42.08        30.81        27.62        38.86 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7844 TCGA-85-8048 
       11.97         6.41        36.53        32.91        29.95        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8351 
       19.04        24.13        31.56        16.87        10.09        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC 
        5.29         3.09         0.10        15.62        25.68        14.96 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7964 
       18.18        12.56        14.96         3.65         2.93        14.07 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
       20.22        22.62        10.59         2.70         3.48         5.26 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-A4JL 
        0.16        11.70        14.14        17.69        18.31        16.57 
TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A7SW 
       27.16        18.58        20.71        19.10        16.11        13.41 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HN 
       11.84         0.07        64.08        51.78        13.74        37.22 
TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NK-A7XE 
       24.00        29.75         0.43 

$`1Q GAIN WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3416 TCGA-18-3419 
        7.46        79.46         4.80        11.34        31.99         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1076 
       86.96         6.18         2.79       154.32        27.19        60.89 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       15.58        31.73       122.43        43.23        31.63        88.11 
TCGA-21-5786 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       33.93        32.19         7.33        14.93         4.31        64.21 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 
       35.08        24.13        34.75        13.12        32.02         9.57 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 
       11.77        31.73        64.93        44.25         0.79        11.74 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 TCGA-33-4589 TCGA-33-6737 
       56.32        16.64         7.63        79.53         1.55        19.76 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-2604 
        0.30        36.62         6.94       118.36        27.16        31.50 
TCGA-34-2605 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 
       28.96        31.27        67.79        56.38         9.07        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-37-3789 TCGA-37-4129 
       30.94         4.96        27.19        26.43         0.43         6.58 
TCGA-37-4130 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5024 
        8.12         6.81         3.39        47.80        44.75        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       60.79         1.71        24.33         1.94        27.39        36.39 
TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 
       35.64        17.88        40.21        27.02        18.38        27.91 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
       24.89         5.46         3.81        19.59        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
       11.77         2.93        11.61        14.20        12.03         9.99 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
       13.91         0.39        29.95         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        0.10        18.25         2.04         0.62         0.99         0.43 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        1.45         1.32         6.51         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 
       26.89        17.00        14.07         1.35        22.75         1.18 
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-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       17.85        21.04        18.74         0.26         2.76         0.03 
TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L 
       13.25        29.95        71.24        16.47        85.12        56.65 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2709 
        3.58        12.23        96.82        37.94        92.71        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       66.54        41.42         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-63-A5MB 
       48.49        42.64         3.19        32.32        23.57       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT 
       70.62        58.65        14.99        11.34        25.28        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-66-2757 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-68-8250 TCGA-77-6842 TCGA-77-6844 
        2.73         6.64         6.94         8.02        29.56        75.09 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 
       42.28        70.13       106.95         6.51        37.81        82.92 
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-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ 
       26.40        27.39        54.41        65.49        35.90       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-6175 TCGA-85-6561 
      132.36       117.57        22.29         5.92         9.67        12.99 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 TCGA-85-8071 
       34.95        31.30         1.38         1.15        18.94        14.07 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8354 TCGA-85-8355 
       34.52         0.76        13.22        22.45        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CN 
        0.72         7.76        14.63        13.94        12.59        19.33 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 
       17.72        24.36        19.73        16.21        15.85         0.79 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-92-8063 TCGA-92-8065 
       12.39        24.92         9.50        11.77         4.01         2.30 
TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-96-7544 
       21.04         4.01         5.03        26.63        16.14        49.87 
TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 
       57.07        17.46        19.36         8.42         2.76        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.67        21.34         3.88        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HH 
       21.21        20.32        12.89        13.18         4.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ 
       45.37         4.21         2.89        39.85        30.58        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N 
       22.78        83.57        65.49         3.65        16.80        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        12.72        43.89         8.58        11.18         0.20 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.07              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           174.08            154.32 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           20.910            18.015 
[1] "0.1 - 174.1 (20.9)" "0.0 - 154.3 (18.0)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         0       27       74        1        23        39
  1Q GAIN WILD-TYPE       2       60       77        1        40        53
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  1Q GAIN MUTATED           0         23          7        6
  1Q GAIN WILD-TYPE         3         39         14        1
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                27                60
  STAGE IB                74                77
  STAGE II                 1                 1
  STAGE IIA               23                40
  STAGE IIB               39                53
  STAGE III                0                 3
  STAGE IIIA              23                39
  STAGE IIIB               7                14
  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    35 128  27  10
  1Q GAIN WILD-TYPE  76 162  42  13
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              35                76
  T2             128               162
  T3              27                42
  T4              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                 N0  N1  N2  N3
  1Q GAIN MUTATED   127  57  13   1
  1Q GAIN WILD-TYPE 185  74  26   4
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0             127               185
  N1              57                74
  N2              13                26
  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   169   6
  1Q GAIN WILD-TYPE 235   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    169    6
  1Q GAIN WILD-TYPE  235    1
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             169               235
  1               6                 1
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    45 155
  1Q GAIN WILD-TYPE  82 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     45  155
  1Q GAIN WILD-TYPE   82  211
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              45                82
  MALE               155               211
[1] 2 2
[1] FALSE
D2V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                      11
  1Q GAIN WILD-TYPE                                     4
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                         0
  1Q GAIN WILD-TYPE                                       1
                   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                                                           188
  1Q GAIN WILD-TYPE                                                         282
D2V9, multiclass
                                                             clus
vv                                                            1Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             188
                                                             clus
vv                                                            1Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               282
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     3 197
  1Q GAIN WILD-TYPE  10 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3  197
  1Q GAIN WILD-TYPE   10  283
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                3                10
  YES             197               283
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED   167   5   1   8
  1Q GAIN WILD-TYPE 227   7   3  14
D2V13, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             167               227
  R1               5                 7
  R2               1                 3
  RX               8                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   142
  1Q GAIN WILD-TYPE     6                        20   198
D2V14, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              11                20
  WHITE                                 142               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"
D2V15, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     4 125
  1Q GAIN WILD-TYPE   4 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4  125
  1Q GAIN WILD-TYPE    4  184
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO             125               184
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED   134  77
  2P GAIN WILD-TYPE 147 119
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              211               266 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               77               119 
$`2P GAIN MUTATED`
TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
       79.46       117.57        11.34        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-21-1072 TCGA-21-1076 TCGA-21-1079 TCGA-21-1081 
        1.64        86.96        99.16        60.89        31.73         9.34 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-21-A5DI TCGA-22-4591 TCGA-22-4595 
       43.23        88.11        33.93        32.19        20.48        24.13 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 
       38.17        13.12        32.02        31.73        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        54.28        71.34        18.84        62.86 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       56.32        22.06         7.63       174.08       103.53       151.27 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 
       27.02         4.70       110.99       118.36         2.63        61.61 
TCGA-34-2604 TCGA-34-2605 TCGA-34-5231 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 
       31.50        28.96        65.23         9.07        12.00        16.93 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       18.15         1.12        27.19         4.04        26.43        20.91 
TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        0.39         8.12         7.82        47.80        74.07        44.75 
TCGA-39-5027 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       60.79        15.58        35.64        35.70        17.06        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
       38.66        27.02        33.11        18.38        27.91        12.36 
TCGA-43-7658 TCGA-43-8115 TCGA-46-3768 TCGA-46-6025 TCGA-51-4080 TCGA-52-7809 
       66.51        13.38         9.99        10.65         0.39         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6546 TCGA-56-7222 
       30.35         8.75        28.96        18.25         0.62         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8308 
        0.99         1.45         0.85         6.51         3.48        17.00 
TCGA-56-8504 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
       16.77        20.25        15.81        19.23        13.32        17.85 
TCGA-56-A5DS TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
        0.26        71.24        16.47        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 TCGA-60-2711 TCGA-60-2712 
       29.92        10.22        96.82        80.45        41.42         9.01 
TCGA-60-2719 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI 
       42.64        23.57        11.77       102.67        66.61        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU 
       59.97        45.57        25.28        89.29        78.28        25.41 
TCGA-63-A5MV TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 TCGA-66-2767 TCGA-66-2770 
       36.16         2.01        21.01        25.05         2.01        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2787 TCGA-66-2789 TCGA-66-2792 
       19.00         3.02         2.01        40.01         4.04        30.02 
TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I 
       10.06         4.01        49.05         2.73         6.64        16.18 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       29.56        23.28        11.18        89.98         0.49        42.28 
TCGA-77-7335 TCGA-77-7337 TCGA-77-8009 TCGA-77-8130 TCGA-77-8136 TCGA-77-8139 
       70.13       106.95        53.95        82.92        39.09       104.09 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GA 
        9.63        54.41         0.33       132.36        42.41        42.08 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86         9.67        11.97         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        16.87        10.09 
TCGA-85-8350 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       22.45        32.71         0.10        15.62        19.33        17.72 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
       19.73        12.56        15.85         3.65         2.93        11.77 
TCGA-90-7964 TCGA-90-A4EE TCGA-92-7341 TCGA-94-7557 TCGA-94-7943 TCGA-94-8490 
       14.07        22.62         3.48         0.16        11.70         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8169 
       26.63        14.14        16.14        17.69        57.07        18.31 
TCGA-96-A4JK TCGA-98-7454 TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       19.36         8.42        27.16        18.58        20.71        19.10 
TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HK 
       16.11        11.84         0.07        51.78         1.22         4.21 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NK-A7XE TCGA-O2-A52V TCGA-O2-A52W 
        2.89        37.22        14.73         0.43        43.89         8.58 
TCGA-XC-AA0X 
        0.20 

$`2P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         7.46        75.75         4.80        31.99         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
        2.79       154.32        49.94        27.19       119.54        46.88 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 
       70.16        34.78        15.58       122.43       119.80        31.63 
TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       41.69        10.82        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 
       64.21         1.74        14.10        27.02        48.82        35.08 
TCGA-22-4594 TCGA-22-4596 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       48.33         0.56        34.75        19.30         9.57        11.77 
TCGA-22-5472 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-33-4533 
       64.93        79.20        11.74        30.12        16.64       133.74 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
       98.01        79.53        14.07        54.44         1.55        19.76 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2608 
        0.30        36.62         6.94        44.19        27.16        32.88 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5929 
       31.27        67.79        56.38        23.24        30.94         4.96 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 
        3.95         0.43         6.58         7.46         6.81         0.39 
TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
        3.39        68.58        55.20        70.03         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5039 TCGA-43-2578 TCGA-43-6647 
        1.94        27.39        36.39        17.88        22.49        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-8116 
       21.47         5.46         3.81        19.59         7.76        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
        2.93        11.61         9.73        14.20        12.03        13.91 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 
        0.39        29.95        28.34        27.45         0.10         2.04 
TCGA-56-7221 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 
        0.99         1.32         0.10        17.49        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         1.18        10.36         9.93 
TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 
       20.94        21.04        18.74         0.13         2.76         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-60-2695 
       13.25        13.55        29.95        34.78        85.12        21.11 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 
        3.58        12.23        37.94        92.71        21.93        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
       66.54        56.91        50.33        35.34        48.49         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MM 
       32.32        29.85        35.90        26.83        70.62        14.99 
TCGA-63-A5MN TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       11.34        16.37        53.88        34.59        16.96        43.10 
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-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
       43.99         0.99         2.01         1.02         2.01         7.07 
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-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-68-7757 
       25.97        22.98        22.98         5.03        54.08         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7140 
        8.02        13.35        14.73        73.12        75.09        20.78 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
        0.16        46.78        15.75         6.51        86.76        37.81 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       12.59        53.92        17.72        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 
        6.97        65.49        35.90       126.18       117.57        22.29 
TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
        5.92        30.81        12.99        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        14.07        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 
        0.72         7.76        14.63        13.94        12.59        25.68 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 
       14.96        24.36        18.18        16.21        14.96         0.79 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 
       12.39        24.92         9.50        20.22        10.59         2.70 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-96-7544 
        4.01         5.26         2.30        21.04         4.01        49.87 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       17.46        16.57         2.76        30.81        30.67        21.34 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        20.32 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HI 
       12.89        13.18        13.41        64.08         4.54        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT 
       13.74        39.85        30.58        24.00        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q 
       83.57        65.49         3.65        16.80        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A5IB 
       12.72        11.18 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           174.08            154.32 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           20.910            17.605 
[1] "0.1 - 174.1 (20.9)" "0.0 - 154.3 (17.6)"
[1] "hr=" "1.5"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         1       31       64        2        32        45
  2P GAIN WILD-TYPE       1       56       87        0        31        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  2P GAIN MUTATED           0         28         10        3
  2P GAIN WILD-TYPE         3         34         11        4
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                31                56
  STAGE IB                64                87
  STAGE II                 2                 0
  STAGE IIA               32                31
  STAGE IIB               45                47
  STAGE III                0                 3
  STAGE IIIA              28                34
  STAGE IIIB              10                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
  2P GAIN MUTATED    42 128  36  12
  2P GAIN WILD-TYPE  69 162  33  11
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              42                69
  T2             128               162
  T3              36                33
  T4              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                 N0  N1  N2  N3
  2P GAIN MUTATED   132  68  15   2
  2P GAIN WILD-TYPE 180  63  24   3
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0             132               180
  N1              68                63
  N2              15                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"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   184   3
  2P GAIN WILD-TYPE 220   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    184    3
  2P GAIN WILD-TYPE  220    4
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0             184               220
  1               3                 4
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    41 177
  2P GAIN WILD-TYPE  86 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     41  177
  2P GAIN WILD-TYPE   86  189
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              41                86
  MALE               177               189
[1] 2 2
[1] FALSE
D3V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                      11
  2P GAIN WILD-TYPE                                     4
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                         1
  2P GAIN WILD-TYPE                                       0
                   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                                                           205
  2P GAIN WILD-TYPE                                                         265
D3V9, multiclass
                                                             clus
vv                                                            2P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             205
                                                             clus
vv                                                            2P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               265
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     8 210
  2P GAIN WILD-TYPE   5 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8  210
  2P GAIN WILD-TYPE    5  270
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                8                 5
  YES             210               270
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, continuous
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED   180   3   1   7
  2P GAIN WILD-TYPE 214   9   3  15
D3V13, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0             180               214
  R1               3                 9
  R2               1                 3
  RX               7                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   158
  2P GAIN WILD-TYPE     5                        21   182
D3V14, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              10                21
  WHITE                                 158               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1 138
  2P GAIN WILD-TYPE   7 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1  138
  2P GAIN WILD-TYPE    7  171
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO             138               171
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    82  53
  2Q GAIN WILD-TYPE 199 143
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              135               342 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               53               143 
$`2Q GAIN MUTATED`
TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-21-1072 TCGA-21-1081 
       79.46       117.57        11.34        23.54        99.16         9.34 
TCGA-21-1083 TCGA-21-A5DI TCGA-22-4595 TCGA-22-4605 TCGA-22-5474 TCGA-22-5477 
       43.23        32.19        24.13        32.02        14.63        44.25 
TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4566 
       71.34        18.84        62.86        56.32         7.63       174.08 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 TCGA-33-AASD TCGA-34-2596 
      103.53       151.27        54.44        27.02       110.99         2.63 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 
       61.61        31.50        28.96         9.07        12.00        16.93 
TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 
        1.12         4.04        20.91         0.39         8.12         7.82 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
       47.80        74.07        44.75        15.58        35.64        35.70 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       17.06        40.21        38.66        27.02        33.11        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-46-3768 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 
       27.91        12.36         9.99         0.39         5.46        30.35 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 
        8.75        28.96        18.25         0.62         0.43         0.99 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8308 TCGA-56-8504 TCGA-56-8629 TCGA-56-A4BX 
        0.85         6.51        17.00        16.77        15.81        13.32 
TCGA-56-A5DS TCGA-58-8391 TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-60-2708 
        0.26        71.24        35.24        29.92        96.82        80.45 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2719 TCGA-60-2726 TCGA-63-A5MI TCGA-63-A5MJ 
       41.42         9.01        42.64        11.77        58.65        59.97 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU TCGA-66-2759 TCGA-66-2770 TCGA-66-2773 
       89.29        78.28        25.41        25.05        23.01         3.02 
TCGA-66-2792 TCGA-66-2793 TCGA-68-7755 TCGA-68-7756 TCGA-77-6842 TCGA-77-6845 
       30.02        10.06         2.73         6.64        29.56        23.28 
TCGA-77-7139 TCGA-77-7142 TCGA-77-8009 TCGA-77-8130 TCGA-77-8139 TCGA-77-8145 
       89.98        42.28        53.95        82.92       104.09         6.97 
TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA 
       54.41         0.33       132.36       117.57        42.41        42.08 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7843 TCGA-85-7844 TCGA-85-8070 
       38.86         9.67        11.97         1.15        29.95        31.56 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8354 TCGA-85-8666 TCGA-85-A4CN 
       10.09         0.76        22.45        32.71        15.62        19.33 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
       19.73        12.56        15.85        11.77        14.07        22.62 
TCGA-92-7341 TCGA-94-7557 TCGA-96-7545 TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J 
        3.48         0.16        57.07        27.16        18.58        20.71 
TCGA-J1-A4AH TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HG TCGA-NC-A5HK TCGA-NC-A5HL 
       19.10        11.84         0.07        51.78         4.21         2.89 
TCGA-NC-A5HN TCGA-NK-A7XE TCGA-O2-A52W 
       37.22         0.43         8.58 

$`2Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 
       12.20         7.46        75.75         4.80        92.15        31.99 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       36.07         1.64        86.96         6.18         2.79       154.32 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 
       49.94        27.19       119.54        46.88        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 
       34.78        15.58        31.73       122.43       119.80        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-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         4.31        64.21         1.74        14.10        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       48.82        20.48        35.08        48.33         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       34.75        13.12        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 
       64.93        63.55         0.79        54.28        79.20        11.74 
TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       30.12        16.64        22.06       133.74        98.01        79.53 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       14.07         1.55        19.76         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2608 TCGA-34-2609 
        6.94        44.19       118.36        27.16        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 
       65.23        67.79        56.38        23.24        30.94        18.15 
TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
        4.96        27.19        26.43         3.95         0.43         6.58 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 
        7.46         6.81         0.39         3.39        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       70.03        60.79         1.71        24.33         1.94        27.39 
TCGA-39-5034 TCGA-39-5039 TCGA-43-2578 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       36.39        17.88        22.49        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        3.81        19.59         7.76        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 
        2.93        11.61         9.73        14.20        12.03        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 
       13.91         0.39        29.95        28.34        27.45         0.10 
TCGA-56-6545 TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 
        2.04         0.99         1.45         1.32         0.10        17.49 
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-A49D TCGA-56-A4BW 
        1.18        10.36         9.93        20.25        20.94        19.23 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 
       17.85        21.04        18.74         0.13         2.76         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-60-2696 TCGA-60-2697 TCGA-60-2698 
       34.36        56.65        21.11         3.58        12.23        10.22 
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-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
       50.33        35.34        48.49         3.19        32.32        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH 
       35.90        23.57        26.83       102.67        70.62        66.61 
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-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        7.07        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-66-2789 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-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 
        6.94         8.02        13.35        16.18        14.73        73.12 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       75.09        11.18        20.78         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        15.75         6.51        86.76        37.81 
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-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G6 
       27.39         9.63        65.49        35.90       126.18        22.29 
TCGA-77-A5G7 TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
        5.92        30.81        27.62        12.99         6.41        36.53 
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-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8288 
       19.04        24.13        14.07        16.87        34.52        13.22 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         5.29         3.09         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB 
       14.63        13.94        12.59         0.10        25.68        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 
       14.96        24.36        18.18        16.21        14.96         0.79 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-A4ED 
       12.39         3.65        24.92         9.50         2.93        20.22 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
       10.59         2.70         4.01         5.26         2.30        21.04 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
       11.70         4.01         5.03        26.63        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       17.69        49.87        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 
        8.42         2.76        30.81        30.67        21.34         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 
       18.15         2.01        27.02        21.21        20.32        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH 
       16.11        13.18        13.41        64.08         4.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       45.37        13.74        39.85        30.58        24.00        14.73 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       29.75        22.78        83.57        65.49         3.65        16.80 
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 
           174.08            154.32 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           23.010            18.165 
[1] "0.1 - 174.1 (23.0)" "0.0 - 154.3 (18.2)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         1       16       44        1        21        29
  2Q GAIN WILD-TYPE       1       71      107        1        42        63
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  2Q GAIN MUTATED           0         16          6        2
  2Q GAIN WILD-TYPE         3         46         15        5
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                16                71
  STAGE IB                44               107
  STAGE II                 1                 1
  STAGE IIA               21                42
  STAGE IIB               29                63
  STAGE III                0                 3
  STAGE IIIA              16                46
  STAGE IIIB               6                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
  2Q GAIN MUTATED    25  85  19   9
  2Q GAIN WILD-TYPE  86 205  50  14
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              25                86
  T2              85               205
  T3              19                50
  T4               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                 N0  N1  N2  N3
  2Q GAIN MUTATED    87  41  10   0
  2Q GAIN WILD-TYPE 225  90  29   5
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              87               225
  N1              41                90
  N2              10                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   113   2
  2Q GAIN WILD-TYPE 291   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED    113    2
  2Q GAIN WILD-TYPE  291    5
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0             113               291
  1               2                 5
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    26 112
  2Q GAIN WILD-TYPE 101 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     26  112
  2Q GAIN WILD-TYPE  101  254
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              26               101
  MALE               112               254
[1] 2 2
[1] FALSE
D4V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED                                       8
  2Q GAIN WILD-TYPE                                     7
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED                                         0
  2Q GAIN WILD-TYPE                                       1
                   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                                                           128
  2Q GAIN WILD-TYPE                                                         342
D4V9, multiclass
                                                             clus
vv                                                            2Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             128
                                                             clus
vv                                                            2Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               342
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     6 132
  2Q GAIN WILD-TYPE   7 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      6  132
  2Q GAIN WILD-TYPE    7  348
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                6                 7
  YES             132               348
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED   113   3   0   3
  2Q GAIN WILD-TYPE 281   9   4  19
D4V13, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0             113               281
  R1               3                 9
  R2               0                 4
  RX               3                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   103
  2Q GAIN WILD-TYPE     6                        24   237
D4V14, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               7                24
  WHITE                                 103               237
[1] 3 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  93
  2Q GAIN WILD-TYPE   7 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   93
  2Q GAIN WILD-TYPE    7  216
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              93               216
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    54  46
  3P GAIN WILD-TYPE 227 150
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              100               377 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               46               150 
$`3P GAIN MUTATED`
TCGA-18-3410 TCGA-18-3414 TCGA-21-1080 TCGA-21-1081 TCGA-22-1000 TCGA-22-1002 
        4.80        23.54       122.43         9.34        14.93         4.31 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-5477 TCGA-22-5485 TCGA-22-5489 
       35.08        24.13        34.75        44.25        30.12        62.86 
TCGA-22-5491 TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 TCGA-33-4586 TCGA-33-A5GW 
       56.32       133.74        98.01       103.53        14.07         0.30 
TCGA-33-AASB TCGA-33-AASD TCGA-34-2609 TCGA-34-5232 TCGA-34-5236 TCGA-34-5240 
        6.94       110.99        31.27        67.79         9.07        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-37-3783 TCGA-39-5019 
       16.93        30.94        18.15         1.12         3.95        44.75 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5029 TCGA-39-5030 TCGA-39-5037 TCGA-39-5040 
       68.58        55.20        24.33         1.94        35.70        17.06 
TCGA-43-3394 TCGA-43-5670 TCGA-43-6771 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
       27.02        27.91         5.46        12.03         9.99        10.65 
TCGA-46-6026 TCGA-52-7810 TCGA-56-5898 TCGA-56-7223 TCGA-56-7730 TCGA-56-8308 
       13.91        30.35        18.25         0.99         6.51        17.00 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8393 TCGA-58-A46J 
       20.94        19.23        18.74         0.13        34.78        85.12 
TCGA-58-A46K TCGA-58-A46M TCGA-60-2703 TCGA-60-2706 TCGA-60-2713 TCGA-60-2715 
       34.36        35.24        96.82        92.71        56.91        35.34 
TCGA-63-A5MB TCGA-63-A5MP TCGA-63-A5MV TCGA-66-2727 TCGA-66-2756 TCGA-66-2766 
      102.67        25.28        36.16        16.96         0.99         1.02 
TCGA-66-2771 TCGA-66-2777 TCGA-77-7140 TCGA-77-8008 TCGA-77-8009 TCGA-77-8136 
       19.00         2.01        20.78        86.76        53.95        39.09 
TCGA-77-8145 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        6.97        54.41       132.36        42.41        42.08        30.81 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 TCGA-85-8049 TCGA-85-8350 TCGA-85-8352 
       27.62        12.99        36.53        19.04        22.45         5.29 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4JC TCGA-94-7033 TCGA-94-7943 
       14.63        13.94         0.10        14.96        21.04        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-96-7545 TCGA-98-8020 TCGA-98-A538 TCGA-98-A53B 
        4.01         5.03        57.07         2.76        27.16         2.01 
TCGA-J1-A4AH TCGA-NC-A5HK TCGA-NC-A5HR TCGA-XC-AA0X 
       19.10         4.21        29.75         0.20 

$`3P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
       92.15        31.99        36.07         1.64        86.96         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
        2.79       154.32        49.94        27.19       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-21-1082 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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 
       10.82        32.19        21.99         7.33        64.21         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 
       14.10        27.02        48.82        20.48        48.33         0.56 
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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 
       31.73        64.93        63.55        14.63         0.79        54.28 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5492 TCGA-22-A5C4 
       71.34        79.20        11.74        18.84        16.64        22.06 
TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 
        7.63        79.53       174.08       151.27        54.44         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASI TCGA-33-AASJ 
       19.76        27.02         4.70        36.62        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       27.16         2.63        61.61        31.50        28.96        32.88 
TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 
       65.23        56.38        23.24         4.96        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       26.43        20.91         0.43         0.39         6.58         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        7.46         7.82         6.81         0.39         3.39        47.80 
TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5031 TCGA-39-5034 
       74.07        70.03        60.79         1.71        27.39        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       15.58        35.64        17.88        40.21        22.49        38.66 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 
       33.11        18.38        12.36        24.89        21.47         3.81 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
       19.59         7.76        66.51        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       11.61         9.73        14.20         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
       28.34         5.46         8.75        27.45        28.96         0.10 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 
        2.04         0.62         0.99         0.43         1.45         1.32 
TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        0.85         0.10        17.49         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
        9.93        20.25        15.81        13.32        17.85        21.04 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26         2.76         0.03        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
       71.24        16.47        56.65        29.92        21.11         3.58 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       12.23        10.22        37.94        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       66.54        41.42         9.01        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        3.19        32.32        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
       11.77        70.62        66.61        58.65        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       14.99        11.34        89.29        78.28        16.37        25.41 
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-68-8250 TCGA-68-8251 TCGA-68-A59I 
        2.73         6.64         6.94         8.02        13.35        16.18 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       14.73        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 
       89.98         0.49        42.28        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        15.75         6.51        37.81        82.92        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 
        9.63        65.49        35.90         0.33       126.18       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 
       22.29         5.92        38.86         9.67        11.97         6.41 
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-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
       18.94        25.15        24.13        31.56        14.07        16.87 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 
       34.52        10.09         0.76        13.22        16.77         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8584 TCGA-85-8666 
       32.71         2.01         0.72         7.76        12.59        15.62 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       25.68        19.33        17.72        24.36        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       12.56        16.21        15.85        14.96         0.79        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
        3.65        24.92         9.50         2.93        11.77        14.07 
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-94-7557 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
        5.26         2.30         0.16        26.63        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       17.69        49.87        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A 
        8.42        30.81        30.67        21.34         3.88        18.15 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       27.02        21.21        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       16.11        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL 
        4.54        51.78         1.22        45.37        13.74         2.89 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
       39.85        37.22        30.58        24.00        14.73        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N 
       83.57        65.49         3.65        16.80         0.43        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
        3.72        12.72        43.89         8.58        11.18 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           133.74            174.08 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            20.99             18.58 
[1] "0.1 - 133.7 (21.0)" "0.0 - 174.1 (18.6)"
[1] "hr=" "1"  
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         0       21       24        1        12        24
  3P GAIN WILD-TYPE       2       66      127        1        51        68
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  3P GAIN MUTATED           0         20          2        1
  3P GAIN WILD-TYPE         3         42         19        6
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                21                66
  STAGE IB                24               127
  STAGE II                 1                 1
  STAGE IIA               12                51
  STAGE IIB               24                68
  STAGE III                0                 3
  STAGE IIIA              20                42
  STAGE IIIB               2                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
  3P GAIN MUTATED    25  58  17   5
  3P GAIN WILD-TYPE  86 232  52  18
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              25                86
  T2              58               232
  T3              17                52
  T4               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                 N0  N1  N2  N3
  3P GAIN MUTATED    61  29  12   0
  3P GAIN WILD-TYPE 251 102  27   5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              61               251
  N1              29               102
  N2              12                27
  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    90   1
  3P GAIN WILD-TYPE 314   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     90    1
  3P GAIN WILD-TYPE  314    6
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              90               314
  1               1                 6
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    21  84
  3P GAIN WILD-TYPE 106 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     21   84
  3P GAIN WILD-TYPE  106  282
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              21               106
  MALE                84               282
[1] 2 2
[1] FALSE
D5V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                       3
  3P GAIN WILD-TYPE                                    12
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                         1
  3P GAIN WILD-TYPE                                       0
                   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                                                           101
  3P GAIN WILD-TYPE                                                         369
D5V9, multiclass
                                                             clus
vv                                                            3P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG CLEAR CELL 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)             101
                                                             clus
vv                                                            3P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               369
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     4 101
  3P GAIN WILD-TYPE   9 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4  101
  3P GAIN WILD-TYPE    9  379
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                4                 9
  YES             101               379
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    82   5   1   4
  3P GAIN WILD-TYPE 312   7   3  18
D5V13, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              82               312
  R1               5                 7
  R2               1                 3
  RX               4                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       3                         9    72
  3P GAIN WILD-TYPE     6                        22   268
D5V14, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               9                22
  WHITE                                  72               268
[1] 3 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  69
  3P GAIN WILD-TYPE   6 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   69
  3P GAIN WILD-TYPE    6  240
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              69               240
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   179 123
  3Q GAIN WILD-TYPE 102  73
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              302               175 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              123                73 
$`3Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 
        7.46        79.46         4.80        23.54        36.07         1.64 
TCGA-18-3421 TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
       86.96         2.79        27.19       119.54        46.88        60.89 
TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       34.78       122.43         9.34        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 
       41.69        33.93        10.82        32.19        21.99        14.93 
TCGA-22-1002 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 
        4.31        14.10        20.48        35.08        24.13        38.17 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 
       34.75        32.02        19.30         9.57        11.77        64.93 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       44.25        54.28        71.34        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       16.64         7.63       133.74        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-A4WN TCGA-33-A5GW 
      103.53        14.07        54.44         1.55         4.70         0.30 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
        6.94       110.99        44.19        27.16         2.63        61.61 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5236 TCGA-34-5240 
       31.50        32.88        31.27        67.79         9.07        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-37-3783 
       16.93        30.94        18.15         1.12         4.04         3.95 
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-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
       74.07        44.75        68.58        55.20        70.03         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 
       24.33         1.94        27.39        15.58        35.70        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       40.21        22.49        27.02        33.11        27.91        12.36 
TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56V TCGA-46-3768 
        5.46         7.76        66.51         2.93        12.03         9.99 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
       10.65        13.91         0.39        29.95         5.46        30.35 
TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
        0.10        18.25         0.99         1.32         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8624 
       17.49         3.48        17.00        14.07        16.77         1.18 
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-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T 
       17.85        21.04        18.74         0.13         0.26         2.76 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
        0.03        13.25        29.95        34.78        85.12        34.36 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       35.24        29.92        21.11        96.82        37.94        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 
       21.93        80.45        66.54         9.01        56.91        35.34 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH 
       32.32        35.90        23.57        11.77       102.67        66.61 
TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       45.57        25.28        89.29        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
       53.88        34.59        16.96        43.10        21.07         0.99 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.92         0.99        21.01        25.05         0.99         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        1.02         2.01        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 
       19.00        12.03         3.98        24.95        25.97        40.01 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 
        4.04        22.98        49.05         2.73         6.64         8.02 
TCGA-68-8251 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 
       13.35        29.56        23.28        11.18        89.98        20.78 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        0.49        42.28        70.13         0.16        46.78        15.75 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       86.76        53.95        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-A5G1 
       11.54        26.40         6.97         9.63        54.41       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
      117.57        22.29         5.92        42.41        42.08        30.81 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86        11.97        12.99         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        16.87        34.52        10.09         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8580 
       22.45        16.77         5.29         3.09         2.01        14.63 
TCGA-85-8582 TCGA-85-8664 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
       13.94         0.10        17.72        14.96        18.18        19.73 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 
       15.85        14.96         3.65         9.50         2.93        14.07 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
       22.62        10.59         4.01         5.26         2.30        21.04 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
       11.70         4.01         5.03        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8021 
       49.87        57.07        17.46        19.36         2.76        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J 
       30.67        27.16        18.15         2.01        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD 
       19.10        12.89        16.11        13.18        11.84         0.07 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN 
       51.78         1.22        45.37         4.21        39.85        37.22 
TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52V 
       24.00        29.75         3.65         0.43        33.07        43.89 
TCGA-O2-A52W TCGA-XC-AA0X 
        8.58         0.20 

$`3Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
       12.20        75.75       117.57        11.34        92.15        31.99 
TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 
        6.18       154.32        49.94        99.16        70.16        15.58 
TCGA-21-1079 TCGA-21-1082 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
       31.73       119.80         7.33        64.21         1.74        27.02 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 
       48.82        48.33         0.56        13.12        31.73        63.55 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-A5C4 
       14.63         0.79        79.20        11.74        18.84        22.06 
TCGA-33-4583 TCGA-33-6737 TCGA-33-6738 TCGA-33-AAS8 TCGA-33-AASJ TCGA-34-2605 
      151.27        19.76        27.02        36.62       118.36        28.96 
TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 
       65.23        56.38        23.24         4.96        27.19        26.43 
TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-39-5011 TCGA-39-5027 
       20.91         0.43         0.39         6.58        47.80        60.79 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 TCGA-43-6647 
       36.39        35.64        17.88        38.66        18.38        24.89 
TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 
       21.47         3.81        19.59        13.38        11.77        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 
        9.73        14.20         0.39        28.34         8.75        27.45 
TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
       28.96         2.04         0.62         0.99         0.43         1.45 
TCGA-56-7582 TCGA-56-8307 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-A4BX 
        0.85        26.89         1.35         1.81        22.75        13.32 
TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46L TCGA-60-2696 TCGA-60-2697 
       13.55        71.24        16.47        56.65         3.58        12.23 
TCGA-60-2698 TCGA-60-2709 TCGA-60-2711 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       10.22        49.48        41.42        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
        3.19        29.85        26.83        70.62        58.65        59.97 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MU TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 
       14.99        11.34        25.41         2.01         1.02         2.01 
TCGA-66-2757 TCGA-66-2768 TCGA-66-2769 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 
       43.99         2.01         7.07        12.00         1.97        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7757 
        5.03        30.02        10.06        54.08         4.01         6.94 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7337 TCGA-77-8007 
       16.18        14.73        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        82.92        12.59        27.39        65.49        35.90 
TCGA-77-8156 TCGA-77-A5FZ TCGA-85-6175 TCGA-85-7698 TCGA-85-7699 TCGA-85-8048 
        0.33       126.18         9.67        31.30        32.91        25.15 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8584 
       31.56        14.07        32.71         0.72         7.76        12.59 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z 
       15.62        25.68        19.33        24.36        12.56        16.21 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-92-7340 
        0.79        12.39        24.92        11.77        20.22         2.70 
TCGA-92-7341 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 
        3.48         0.16        16.14        18.31        16.57         8.42 
TCGA-98-8023 TCGA-98-A539 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-LA-A7SW 
       21.34         3.88        27.02        21.21        20.32        13.41 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HQ 
       64.08         4.54        13.74         2.89        30.58        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S 
       22.78        83.57        65.49        16.80         3.72        12.72 
TCGA-O2-A5IB 
       11.18 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.03              0.16 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           174.08            154.32 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            19.07             19.33 
[1] "0.0 - 174.1 (19.1)" "0.2 - 154.3 (19.3)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         2       60       95        2        36        56
  3Q GAIN WILD-TYPE       0       27       56        0        27        36
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  3Q GAIN MUTATED           0         40         12        7
  3Q GAIN WILD-TYPE         3         22          9        0
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                60                27
  STAGE IB                95                56
  STAGE II                 2                 0
  STAGE IIA               36                27
  STAGE IIB               56                36
  STAGE III                0                 3
  STAGE IIIA              40                22
  STAGE IIIB              12                 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    75 185  38  13
  3Q GAIN WILD-TYPE  36 105  31  10
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              75                36
  T2             185               105
  T3              38                31
  T4              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                 N0  N1  N2  N3
  3Q GAIN MUTATED   198  80  25   4
  3Q GAIN WILD-TYPE 114  51  14   1
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0             198               114
  N1              80                51
  N2              25                14
  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   254   7
  3Q GAIN WILD-TYPE 150   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    254    7
  3Q GAIN WILD-TYPE  150    0
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0             254               150
  1               7                 0
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    78 233
  3Q GAIN WILD-TYPE  49 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     78  233
  3Q GAIN WILD-TYPE   49  133
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              78                49
  MALE               233               133
[1] 2 2
[1] FALSE
D6V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                      12
  3Q GAIN WILD-TYPE                                     3
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                         1
  3Q GAIN WILD-TYPE                                       0
                   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                                                           297
  3Q GAIN WILD-TYPE                                                         173
D6V9, multiclass
                                                             clus
vv                                                            3Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             297
                                                             clus
vv                                                            3Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               173
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    10 301
  3Q GAIN WILD-TYPE   3 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     10  301
  3Q GAIN WILD-TYPE    3  179
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               10                 3
  YES             301               179
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED   251   7   3  14
  3Q GAIN WILD-TYPE 143   5   1   8
D6V13, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0             251               143
  R1               7                 5
  R2               3                 1
  RX              14                 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                        21   214
  3Q GAIN WILD-TYPE     5                        10   126
D6V14, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              21                10
  WHITE                                 214               126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5 195
  3Q GAIN WILD-TYPE   3 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5  195
  3Q GAIN WILD-TYPE    3  114
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             195               114
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    13  16
  4P GAIN WILD-TYPE 268 180
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               29               448 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               16               180 
$`4P GAIN MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-1017 TCGA-22-4591 TCGA-22-4601 
       79.46         4.80        31.99        48.82        20.48        34.75 
TCGA-22-5478 TCGA-22-A5C4 TCGA-34-2596 TCGA-34-2609 TCGA-37-4130 TCGA-43-2576 
        0.79        22.06         2.63        31.27         8.12        40.21 
TCGA-43-3920 TCGA-43-8116 TCGA-56-1622 TCGA-60-2715 TCGA-63-A5MG TCGA-63-A5MV 
       33.11        11.77        28.96        35.34        70.62        36.16 
TCGA-66-2763 TCGA-68-8250 TCGA-77-6842 TCGA-77-7337 TCGA-77-8007 TCGA-77-A5G6 
        0.99         8.02        29.56       106.95         6.51        22.29 
TCGA-85-A4JC TCGA-90-7767 TCGA-94-A4VJ TCGA-96-7545 TCGA-98-8022 
       14.96         2.93        14.14        57.07        30.67 

$`4P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20         7.46        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       92.15        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
      154.32        49.94        27.19       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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       33.93        10.82        32.19        21.99         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 
        4.31        64.21         1.74        14.10        27.02        35.08 
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-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
       14.63        44.25        54.28        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 
       18.84        30.12        62.86        56.32        16.64         7.63 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
      133.74        98.01        79.53       174.08       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
       14.07        54.44         1.55        19.76        27.02         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-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 
       27.16        61.61        31.50        28.96        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       67.79        56.38         9.07        23.24        12.00        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       30.94        18.15         4.96         1.12        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       26.43        20.91         3.95         0.43         0.39         6.58 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        7.46         7.82         6.81         0.39         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       74.07        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1.71        24.33         1.94        27.39        36.39        15.58 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 
       35.64        35.70        17.88        17.06        22.49        38.66 
TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       27.02        18.38        27.91        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
        5.46         3.81        19.59         7.76        66.51        13.38 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
        2.93        11.61         9.73        14.20        12.03         9.99 
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-56-5897 TCGA-56-5898 
        5.46        30.35         8.75        27.45         0.10        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
        2.04         0.62         0.99         0.43         0.99         1.45 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        1.32         0.85         6.51         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
       26.89        17.00        14.07         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.94        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         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-60-2696 TCGA-60-2697 
       56.65        35.24        29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
       49.48        66.54        41.42         9.01        56.91        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
       48.49        42.64         3.19        32.32        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI 
       23.57        26.83        11.77       102.67        66.61        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-A5MU TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        25.41        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-66-2758 TCGA-66-2759 TCGA-66-2765 
        0.92         0.99        43.99        21.01        25.05         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-66-2773 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-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         5.03        30.02        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-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       14.73        73.12        75.09        23.28        11.18        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 
       20.78         0.49        42.28        70.13         0.16        46.78 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
       15.75        86.76        53.95        37.81        82.92        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         9.63        54.41        65.49        35.90 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
        0.33       126.18       132.36       117.57         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       42.08        30.81        27.62        38.86         9.67        11.97 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       12.99         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-85-8276 TCGA-85-8277 
       24.13        31.56        14.07        16.87        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-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       32.71         2.01         0.72         7.76        14.63        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       12.59         0.10        15.62        25.68        19.33        17.72 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        18.18        19.73        12.56        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       14.96         0.79        12.39         3.65        24.92         9.50 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       11.77        14.07        20.22        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        3.48         4.01         5.26         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 
       11.70         4.01         5.03        26.63        16.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
       49.87        18.31        17.46        19.36        16.57         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
        2.76        30.81        21.34        27.16         3.88        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
        2.01        27.02        21.21        20.32        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       19.10        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
        0.07        64.08         4.54        51.78         1.22        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO 
       13.74         4.21         2.89        39.85        37.22        30.58 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       24.00        14.73        29.75        22.78        83.57        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
        3.65        16.80         0.43        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89         8.58        11.18         0.20 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.79              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           106.95            174.08 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            28.96             18.97 
[1] "0.8 - 107.0 (29.0)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.3"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         0        7        6        0         4         8
  4P GAIN WILD-TYPE       2       80      145        2        59        84
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  4P GAIN MUTATED           0          6          0        0
  4P GAIN WILD-TYPE         3         56         21        7
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 7                80
  STAGE IB                 6               145
  STAGE II                 0                 2
  STAGE IIA                4                59
  STAGE IIB                8                84
  STAGE III                0                 3
  STAGE IIIA               6                56
  STAGE IIIB               0                21
  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  18   3   2
  4P GAIN WILD-TYPE 102 272  66  21
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               9               102
  T2              18               272
  T3               3                66
  T4               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                 N0  N1  N2  N3
  4P GAIN MUTATED    21   8   3   0
  4P GAIN WILD-TYPE 291 123  36   5
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              21               291
  N1               8               123
  N2               3                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"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    29   0
  4P GAIN WILD-TYPE 375   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     29    0
  4P GAIN WILD-TYPE  375    7
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              29               375
  1               0                 7
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4  28
  4P GAIN WILD-TYPE 123 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4   28
  4P GAIN WILD-TYPE  123  338
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               4               123
  MALE                28               338
[1] 2 2
[1] FALSE
D7V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED                                       1
  4P GAIN WILD-TYPE                                    14
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED                                         1
  4P GAIN WILD-TYPE                                       0
                   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                                                         440
D7V9, multiclass
                                                             clus
vv                                                            4P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG CLEAR CELL 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 CLEAR CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               440
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  31
  4P GAIN WILD-TYPE  12 449
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   31
  4P GAIN WILD-TYPE   12  449
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                12
  YES              31               449
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    25   1   0   2
  4P GAIN WILD-TYPE 369  11   4  20
D7V13, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              25               369
  R1               1                11
  R2               0                 4
  RX               2                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
  4P GAIN MUTATED       1                         2    19
  4P GAIN WILD-TYPE     8                        29   321
D7V14, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               2                29
  WHITE                                  19               321
[1] 3 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  18
  4P GAIN WILD-TYPE   8 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   18
  4P GAIN WILD-TYPE    8  291
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              18               291
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    10  12
  4Q GAIN WILD-TYPE 271 184
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               22               455 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               12               184 
$`4Q GAIN MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-4593 TCGA-22-4601 TCGA-22-5478 
       79.46         4.80        31.99        35.08        34.75         0.79 
TCGA-22-A5C4 TCGA-33-6738 TCGA-34-2596 TCGA-34-2609 TCGA-34-8456 TCGA-43-2576 
       22.06        27.02         2.63        31.27        26.43        40.21 
TCGA-43-3920 TCGA-56-1622 TCGA-56-7579 TCGA-60-2715 TCGA-63-A5MV TCGA-77-7337 
       33.11        28.96         1.45        35.34        36.16       106.95 
TCGA-85-A4JC TCGA-85-A5B5 TCGA-96-7545 TCGA-O2-A52N 
       14.96         3.65        57.07        33.07 

$`4Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20         7.46        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       92.15        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
      154.32        49.94        27.19       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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       33.93        10.82        32.19        21.99         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
        4.31        64.21         1.74        14.10        27.02        48.82 
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-22-4613 TCGA-22-5471 TCGA-22-5472 
       32.02        19.30         9.57        11.77        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       63.55        14.63        44.25        54.28        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-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
        7.63       133.74        98.01        79.53       174.08       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-A4WN 
      151.27        14.07        54.44         1.55        19.76         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-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 
       27.16        61.61        31.50        28.96        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       67.79        56.38         9.07        23.24        12.00        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       30.94        18.15         4.96         1.12        27.19         4.04 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       20.91         3.95         0.43         0.39         6.58         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        7.46         7.82         6.81         0.39         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       74.07        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1.71        24.33         1.94        27.39        36.39        15.58 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 
       35.64        35.70        17.88        17.06        22.49        38.66 
TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       27.02        18.38        27.91        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
        5.46         3.81        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
       11.77         2.93        11.61         9.73        14.20        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.99        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         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
       18.25         2.04         0.62         0.99         0.43         0.99 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        1.32         0.85         6.51         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
       26.89        17.00        14.07         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.94        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         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-60-2696 TCGA-60-2697 
       56.65        35.24        29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
       49.48        66.54        41.42         9.01        56.91        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
       48.49        42.64         3.19        32.32        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH 
       23.57        26.83        11.77       102.67        70.62        66.61 
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-A5MT TCGA-63-A5MU TCGA-63-A5MW TCGA-63-A5MY 
       89.29        78.28        16.37        25.41        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-66-2791 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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
        8.02        13.35        16.18        14.73        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       75.09        23.28        11.18        89.98        20.78         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       42.28        70.13         0.16        46.78        15.75         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       86.76        53.95        37.81        82.92        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         9.63        54.41        65.49        35.90         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       117.57        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       42.08        30.81        27.62        38.86         9.67        11.97 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       12.99         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-85-8276 TCGA-85-8277 
       24.13        31.56        14.07        16.87        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-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       32.71         2.01         0.72         7.76        14.63        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       12.59         0.10        15.62        25.68        19.33        17.72 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        18.18        19.73        12.56        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
       14.96         0.79        12.39        24.92         9.50         2.93 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       11.77        14.07        20.22        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        3.48         4.01         5.26         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
       11.70         4.01         5.03        26.63        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       17.69        49.87        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
        8.42         2.76        30.81        30.67        21.34        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       18.58        20.71        19.10        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       13.41        11.84         0.07        64.08         4.54        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
        1.22        45.37        13.74         4.21         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT 
       37.22        30.58        24.00        14.73        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q 
       83.57        65.49         3.65        16.80         0.43         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89         8.58        11.18         0.20 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.79              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           106.95            174.08 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            31.63             18.84 
[1] "0.8 - 107.0 (31.6)" "0.0 - 174.1 (18.8)"
[1] "hr=" "1.2"
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       84      148        2        58        87
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  4Q GAIN MUTATED           0          5          0        0
  4Q GAIN WILD-TYPE         3         57         21        7
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 3                84
  STAGE IB                 3               148
  STAGE II                 0                 2
  STAGE IIA                5                58
  STAGE IIB                5                87
  STAGE III                0                 3
  STAGE IIIA               5                57
  STAGE IIIB               0                21
  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     5  15   2   1
  4Q GAIN WILD-TYPE 106 275  67  22
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               5               106
  T2              15               275
  T3               2                67
  T4               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                 N0  N1  N2  N3
  4Q GAIN MUTATED    14   7   2   0
  4Q GAIN WILD-TYPE 298 124  37   5
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              14               298
  N1               7               124
  N2               2                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"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    20   0
  4Q GAIN WILD-TYPE 384   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     20    0
  4Q GAIN WILD-TYPE  384    7
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              20               384
  1               0                 7
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  20
  4Q GAIN WILD-TYPE 124 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   20
  4Q GAIN WILD-TYPE  124  346
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               3               124
  MALE                20               346
[1] 2 2
[1] FALSE
D8V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED                                       1
  4Q GAIN WILD-TYPE                                    14
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED                                         1
  4Q GAIN WILD-TYPE                                       0
                   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                                                            21
  4Q GAIN WILD-TYPE                                                         449
D8V9, multiclass
                                                             clus
vv                                                            4Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG CLEAR CELL 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)              21
                                                             clus
vv                                                            4Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               449
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  22
  4Q GAIN WILD-TYPE  12 458
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   22
  4Q GAIN WILD-TYPE   12  458
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1                12
  YES              22               458
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    19   0   0   1
  4Q GAIN WILD-TYPE 375  12   4  21
D8V13, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              19               375
  R1               0                12
  R2               0                 4
  RX               1                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
  4Q GAIN MUTATED       0                         1    16
  4Q GAIN WILD-TYPE     9                        30   324
D8V14, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               1                30
  WHITE                                  16               324
[1] 3 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   8 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   13
  4Q GAIN WILD-TYPE    8  296
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              13               296
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   172 125
  5P GAIN WILD-TYPE 109  71
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              297               180 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              125                71 
$`5P GAIN MUTATED`
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 
      117.57        11.34        23.54        92.15        36.07        86.96 
TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 
       49.94        46.88        99.16        34.78       122.43         9.34 
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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
       32.19        21.99         7.33         4.31         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-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 
       38.17        34.75         9.57        11.77        31.73        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5483 TCGA-22-5492 
       14.63        44.25         0.79        11.74        18.84        16.64 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 
       22.06       133.74       174.08       103.53       151.27        54.44 
TCGA-33-6738 TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 
       27.02        36.62         6.94        44.19       118.36         2.63 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5236 TCGA-34-5239 
       61.61        31.50        32.88        31.27         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8455 
       12.00        16.93        18.15         4.96         1.12         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4133 TCGA-37-4135 
       26.43        20.91         3.95         0.39         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 
        0.39         3.39        47.80        74.07        68.58        55.20 
TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
       70.03        24.33         1.94        27.39        15.58        35.64 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       17.88        40.21        38.66        27.02        33.11        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
       27.91        12.36        24.89        19.59         7.76        66.51 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
       11.77        11.61        14.20        12.03         9.99        10.65 
TCGA-46-6026 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 
       13.91        29.95        28.34         5.46         8.75        28.96 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 
        2.04         0.62         0.43         1.32         0.85         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
       17.49         3.48        17.00        14.07         1.35        16.77 
TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
        1.18         9.93        20.25        15.81        19.23        13.32 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 
       17.85        21.04         0.13         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-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-60-2711 TCGA-60-2712 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       41.42         9.01        50.33        42.64         3.19        32.32 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH 
       35.90        23.57        26.83        11.77       102.67        66.61 
TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MU 
       58.65        45.57        11.34        25.28        78.28        25.41 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       36.16        53.88        16.96         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 
        1.02         0.99        43.99        21.01        25.05         1.02 
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-66-2782 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2792 
       12.03        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 
       42.28       106.95         0.16        46.78        15.75         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
       86.76        53.95        37.81        82.92        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 TCGA-77-8150 TCGA-77-8156 
       17.72       104.09        26.40         6.97        54.41         0.33 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
      132.36        22.29         5.92        42.41        42.08        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 
       38.86         9.67        11.97         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        14.07        16.87 
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         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       14.63        13.94         0.10        15.62        19.33        17.72 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       14.96        18.18        19.73        12.56        16.21        15.85 
TCGA-85-A511 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
       14.96         9.50         2.93        11.77        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7557 TCGA-94-8035 TCGA-94-A4VJ 
        2.70         3.48         5.26         0.16         4.01        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       17.69        49.87        57.07        18.31        17.46        19.36 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53B 
        2.76        30.81        30.67        21.34         3.88         2.01 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       18.58        20.71        19.10        12.89        16.11        13.18 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN 
       11.84         0.07         4.54        13.74         4.21        37.22 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE 
       14.73        22.78        83.57        65.49         3.65         0.43 
TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       43.89         8.58         0.20 

$`5P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 
       12.20         7.46        75.75        79.46         4.80        31.99 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
        1.64         6.18         2.79       154.32        27.19       119.54 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-22-1000 
       70.16        60.89        15.58        31.73       119.80        14.93 
TCGA-22-1005 TCGA-22-1017 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5472 
       64.21        48.82        13.12        32.02        19.30        64.93 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       54.28        71.34        79.20        30.12        62.86        56.32 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 
        7.63        98.01        79.53        14.07         1.55        19.76 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASL TCGA-34-2605 TCGA-34-5231 
        4.70         0.30       110.99        27.16        28.96        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 
       67.79        56.38        30.94        27.19         0.43         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 TCGA-39-5034 
        8.12         7.46        44.75        60.79         1.71        36.39 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       35.70        17.06        22.49        21.47         5.46         3.81 
TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 TCGA-51-4079 TCGA-51-4080 TCGA-52-7810 
       13.38         2.93         9.73         0.39         0.39        30.35 
TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 
       27.45         0.10        18.25         0.99         0.99         1.45 
TCGA-56-7730 TCGA-56-8307 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-A49D 
        6.51        26.89         1.81        22.75        10.36        20.94 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8393 TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 
       18.74         2.76        34.78        56.65         3.58        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-60-2715 TCGA-60-2716 TCGA-60-2722 TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5MM 
       35.34        48.49        29.85        70.62        59.97        14.99 
TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2734 TCGA-66-2754 TCGA-66-2755 
       89.29        16.37        34.59        43.10         2.01         0.92 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2781 TCGA-66-2783 
        0.99         2.01         2.01         2.01         3.98        24.95 
TCGA-66-2785 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-68-7755 
        1.97         4.04        22.98         5.03        10.06         2.73 
TCGA-68-8250 TCGA-68-8251 TCGA-77-6843 TCGA-77-7139 TCGA-77-7140 TCGA-77-7335 
        8.02        13.35        73.12        89.98        20.78        70.13 
TCGA-77-8131 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 
       12.59        11.54        27.39         9.63        65.49        35.90 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GB TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 
      126.18       117.57        30.81        12.99        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        25.68 
TCGA-85-A4PA TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7964 
       24.36         0.79        12.39         3.65        24.92        14.07 
TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-8490 
       20.22         4.01         2.30        21.04        11.70         5.03 
TCGA-94-8491 TCGA-94-A5I4 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A538 TCGA-98-A53A 
       26.63        16.14        16.57         8.42        27.16        18.15 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-LA-A7SW TCGA-NC-A5HE TCGA-NC-A5HG 
       27.02        21.21        20.32        13.41        64.08        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP 
        1.22        45.37         2.89        39.85        30.58        24.00 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB 
       29.75        16.80        33.07         3.72        12.72        11.18 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           174.08            154.32 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            18.38             20.86 
[1] "0.0 - 174.1 (18.4)" "0.1 - 154.3 (20.9)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         1       54       95        2        38        59
  5P GAIN WILD-TYPE       1       33       56        0        25        33
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  5P GAIN MUTATED           0         38         12        5
  5P GAIN WILD-TYPE         3         24          9        2
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                54                33
  STAGE IB                95                56
  STAGE II                 2                 0
  STAGE IIA               38                25
  STAGE IIB               59                33
  STAGE III                0                 3
  STAGE IIIA              38                24
  STAGE IIIB              12                 9
  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    64 186  40  15
  5P GAIN WILD-TYPE  47 104  29   8
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              64                47
  T2             186               104
  T3              40                29
  T4              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                 N0  N1  N2  N3
  5P GAIN MUTATED   200  76  27   1
  5P GAIN WILD-TYPE 112  55  12   4
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0             200               112
  N1              76                55
  N2              27                12
  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   251   5
  5P GAIN WILD-TYPE 153   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    251    5
  5P GAIN WILD-TYPE  153    2
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             251               153
  1               5                 2
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    76 229
  5P GAIN WILD-TYPE  51 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     76  229
  5P GAIN WILD-TYPE   51  137
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              76                51
  MALE               229               137
[1] 2 2
[1] FALSE
D9V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                       8
  5P GAIN WILD-TYPE                                     7
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                         1
  5P GAIN WILD-TYPE                                       0
                   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                                                           293
  5P GAIN WILD-TYPE                                                         177
D9V9, multiclass
                                                             clus
vv                                                            5P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             293
                                                             clus
vv                                                            5P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               177
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     7 298
  5P GAIN WILD-TYPE   6 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7  298
  5P GAIN WILD-TYPE    6  182
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                7                 6
  YES             298               182
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, continuous
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED   251   6   3   8
  5P GAIN WILD-TYPE 143   6   1  14
D9V13, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             251               143
  R1               6                 6
  R2               3                 1
  RX               8                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       3                        18   213
  5P GAIN WILD-TYPE     6                        13   127
D9V14, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              18                13
  WHITE                                 213               127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3 193
  5P GAIN WILD-TYPE   5 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  193
  5P GAIN WILD-TYPE    5  116
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO             193               116
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    50  41
  5Q GAIN WILD-TYPE 231 155
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               91               386 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               41               155 
$`5Q GAIN MUTATED`
TCGA-18-5592 TCGA-21-1071 TCGA-21-1083 TCGA-21-5782 TCGA-21-A5DI TCGA-22-1012 
       49.94        46.88        43.23        31.63        32.19        14.10 
TCGA-22-1016 TCGA-22-4595 TCGA-22-4596 TCGA-22-5478 TCGA-22-5482 TCGA-22-5483 
       27.02        24.13         0.56         0.79        11.74        18.84 
TCGA-22-A5C4 TCGA-33-4582 TCGA-33-4583 TCGA-33-AASB TCGA-34-2596 TCGA-34-5236 
       22.06       103.53       151.27         6.94         2.63         9.07 
TCGA-34-5241 TCGA-34-5928 TCGA-34-A5IX TCGA-37-3792 TCGA-37-5819 TCGA-39-5021 
       16.93        18.15        20.91         0.39         3.39        68.58 
TCGA-39-5039 TCGA-43-3920 TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 TCGA-43-A56V 
       17.88        33.11        12.36         7.76        66.51        12.03 
TCGA-56-1622 TCGA-56-7222 TCGA-56-7580 TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 
       28.96         0.43         1.32         1.35         1.18         9.93 
TCGA-58-8386 TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-60-2712 TCGA-60-2719 
        0.03        35.24        29.92        96.82         9.01        42.64 
TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MN TCGA-63-A5MV 
       23.57        26.83        66.61        58.65        11.34        36.16 
TCGA-66-2771 TCGA-66-2778 TCGA-66-2786 TCGA-66-2792 TCGA-77-6842 TCGA-77-6844 
       19.00        19.00        25.97        30.02        29.56        75.09 
TCGA-77-7138 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
       11.18        42.28       106.95        46.78        15.75        86.76 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G7 
       82.92        53.92        54.41         0.33        22.29         5.92 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-7699 TCGA-85-8048 TCGA-85-8350 TCGA-85-8582 
       27.62         9.67        32.91        25.15        22.45        13.94 
TCGA-85-A4QQ TCGA-85-A510 TCGA-90-7769 TCGA-90-A59Q TCGA-92-7340 TCGA-96-8169 
       18.18        15.85        11.77        10.59         2.70        18.31 
TCGA-96-8170 TCGA-98-8020 TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       17.46         2.76        18.58        20.71        19.10        12.89 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HN TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A7XE 
       13.18        11.84        37.22        22.78        83.57         0.43 
TCGA-XC-AA0X 
        0.20 

$`5Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       11.34        23.54        92.15        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
       86.96         6.18         2.79       154.32        27.19       119.54 
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-21-5783 TCGA-21-5784 TCGA-21-5786 
      122.43         9.34       119.80        88.11        41.69        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       10.82        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 
        1.74        48.82        20.48        35.08        48.33        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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
       31.73        64.93        63.55        14.63        44.25        54.28 
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-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 
        7.63       133.74        98.01        79.53       174.08        14.07 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       54.44         1.55        19.76        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 
       36.62       110.99        44.19       118.36        27.16        61.61 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
       31.50        28.96        32.88        31.27        65.23        67.79 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
       56.38        23.24        12.00        30.94         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
       27.19         4.04        26.43         3.95         0.43         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 
        8.12         7.46         7.82         6.81         0.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
       74.07        44.75        55.20        70.03        60.79         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        27.39        36.39        15.58        35.64 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
       35.70        17.06        40.21        22.49        38.66        27.02 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       18.38        27.91        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
       19.59        13.38        11.77         2.93        11.61         9.73 
TCGA-43-A56U TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       14.20         9.99        10.65        13.91         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
       29.95        28.34         5.46        30.35         8.75        27.45 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7223 
        0.10        18.25         2.04         0.62         0.99         0.99 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        1.45         0.85         6.51         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
       26.89        17.00        14.07        16.77         1.81        22.75 
TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
       10.36        20.25        15.81        20.94        19.23        13.32 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T 
       17.85        21.04        18.74         0.13         0.26         2.76 
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-60-2696 TCGA-60-2697 
       85.12        34.36        56.65        21.11         3.58        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-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       66.54        41.42        56.91        50.33        35.34        48.49 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 TCGA-63-A5MB 
        3.19        32.32        29.85        35.90        11.77       102.67 
TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MP TCGA-63-A5MR 
       70.62        59.97        45.57        14.99        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        25.41        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-66-2758 TCGA-66-2759 TCGA-66-2763 
        0.92         0.99        43.99        21.01        25.05         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-66-2773 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-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
        1.97        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       10.06        54.08         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 
        6.94         8.02        13.35        16.18        14.73        73.12 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7338 
       23.28        89.98        20.78         0.49        70.13         0.16 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 
        6.51        53.95        37.81        12.59        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         9.63 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G8 
       65.49        35.90       126.18       132.36       117.57        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
       42.08        30.81        38.86        11.97        12.99         6.41 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       36.53        34.95        31.30         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
       18.94        19.04        24.13        31.56        14.07        16.87 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
       34.52        10.09         0.76        13.22        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         0.72         7.76        14.63 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       12.59         0.10        15.62        25.68        19.33        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
       14.96        24.36        19.73        12.56        16.21        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        0.79        12.39         3.65        24.92         9.50         2.93 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       14.07        20.22        22.62         3.48         4.01         5.26 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.30        21.04         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       26.63        14.14        16.14        17.69        49.87        57.07 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       19.36        16.57         8.42        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       27.16         3.88        18.15         2.01        27.02        21.21 
TCGA-98-A53H TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       20.32        16.11        13.41         0.07        64.08         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       51.78         1.22        45.37        13.74         4.21         2.89 
TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CT 
       39.85        30.58        24.00        14.73        29.75        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
        3.65        16.80        33.07         3.72        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB 
        8.58        11.18 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           151.27            174.08 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           19.000            19.265 
[1] "0.0 - 151.3 (19.0)" "0.1 - 174.1 (19.3)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         0       16       28        0        13        20
  5Q GAIN WILD-TYPE       2       71      123        2        50        72
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  5Q GAIN MUTATED           0         11          2        1
  5Q GAIN WILD-TYPE         3         51         19        6
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                16                71
  STAGE IB                28               123
  STAGE II                 0                 2
  STAGE IIA               13                50
  STAGE IIB               20                72
  STAGE III                0                 3
  STAGE IIIA              11                51
  STAGE IIIB               2                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
  5Q GAIN MUTATED    21  56  13   2
  5Q GAIN WILD-TYPE  90 234  56  21
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              21                90
  T2              56               234
  T3              13                56
  T4               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                 N0  N1  N2  N3
  5Q GAIN MUTATED    57  26   7   1
  5Q GAIN WILD-TYPE 255 105  32   4
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              57               255
  N1              26               105
  N2               7                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    78   1
  5Q GAIN WILD-TYPE 326   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     78    1
  5Q GAIN WILD-TYPE  326    6
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              78               326
  1               1                 6
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    21  71
  5Q GAIN WILD-TYPE 106 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     21   71
  5Q GAIN WILD-TYPE  106  295
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              21               106
  MALE                71               295
[1] 2 2
[1] FALSE
D10V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED                                       2
  5Q GAIN WILD-TYPE                                    13
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED                                         1
  5Q GAIN WILD-TYPE                                       0
                   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                                                            89
  5Q GAIN WILD-TYPE                                                         381
D10V9, multiclass
                                                             clus
vv                                                            5Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG CLEAR CELL 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)              89
                                                             clus
vv                                                            5Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               381
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     2  90
  5Q GAIN WILD-TYPE  11 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2   90
  5Q GAIN WILD-TYPE   11  390
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                2                11
  YES              90               390
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    75   2   1   1
  5Q GAIN WILD-TYPE 319  10   3  21
D10V13, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              75               319
  R1               2                10
  R2               1                 3
  RX               1                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
  5Q GAIN MUTATED       0                         5    65
  5Q GAIN WILD-TYPE     9                        26   275
D10V14, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               5                26
  WHITE                                  65               275
[1] 3 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     0  56
  5Q GAIN WILD-TYPE   8 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   56
  5Q GAIN WILD-TYPE    8  253
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              56               253
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    61  44
  6P GAIN WILD-TYPE 220 152
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              105               372 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               44               152 
$`6P GAIN MUTATED`
TCGA-18-3409 TCGA-21-1072 TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 
       79.46        99.16        34.78        31.73       119.80        43.23 
TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 
       33.93        10.82         4.31        34.75        32.02        19.30 
TCGA-22-5482 TCGA-33-4533 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 TCGA-33-AAS8 
       11.74       133.74       103.53        54.44         1.55        36.62 
TCGA-33-AASI TCGA-34-2609 TCGA-34-5928 TCGA-34-7107 TCGA-37-4132 TCGA-37-4133 
       44.19        31.27        18.15         1.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 TCGA-39-5022 TCGA-43-2578 TCGA-43-5670 
        6.81         0.39        44.75        55.20        22.49        27.91 
TCGA-43-6770 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 
       21.47        13.91         5.46        30.35        28.96        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7730 TCGA-56-7822 TCGA-56-8308 TCGA-56-8629 
        2.04         0.62         6.51        17.49        17.00        15.81 
TCGA-56-A49D TCGA-58-8387 TCGA-58-8393 TCGA-58-A46K TCGA-60-2703 TCGA-60-2714 
       20.94        13.25        34.78        34.36        96.82        50.33 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MH TCGA-63-A5MI 
       35.34        42.64        35.90        26.83        66.61        58.65 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2734 TCGA-66-2754 TCGA-66-2757 
       78.28        16.37        53.88        43.10         2.01        43.99 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 TCGA-66-2777 TCGA-66-2781 
       25.05         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        42.28        15.75 
TCGA-77-8130 TCGA-77-8156 TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7699 
       82.92         0.33         9.67        11.97         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        16.87        34.52         0.76         3.09 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB TCGA-90-A4EE TCGA-90-A59Q TCGA-94-7943 
       13.94        12.59        17.72        22.62        10.59        11.70 
TCGA-98-7454 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B TCGA-LA-A446 TCGA-LA-A7SW 
        8.42        30.67        27.16         2.01        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HK TCGA-NC-A5HM 
       11.84         0.07        64.08        51.78         4.21        39.85 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-O2-A52W 
       29.75        22.78         8.58 

$`6P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75         4.80       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       23.54        92.15        31.99        36.07         1.64        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
        6.18         2.79       154.32        49.94        27.19       119.54 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
       46.88        70.16        60.89        15.58       122.43         9.34 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
       31.63        88.11        41.69        32.19        21.99         7.33 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
       14.93        64.21         1.74        14.10        27.02        48.82 
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-22-4604 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       13.12         9.57        11.77        31.73        64.93        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        54.28        71.34        79.20 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       18.84        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
        7.63        98.01        79.53       174.08       151.27        14.07 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD 
       19.76        27.02         4.70         0.30         6.94       110.99 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       32.88        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 
       12.00        16.93        30.94         4.96        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       26.43        20.91         3.95         0.43         0.39         6.58 
TCGA-37-4130 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 
        8.12         3.39        47.80        74.07        68.58        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       60.79         1.71        24.33         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
       15.58        35.64        35.70        17.88        17.06        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 
       38.66        27.02        33.11        18.38        12.36        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
        5.46         3.81        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
       11.77         2.93        11.61         9.73        14.20        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        9.99        10.65         0.39         0.39        29.95        28.34 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
        8.75        27.45         0.10         0.99         0.43         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        1.45         1.32         0.85         0.10         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       14.07         1.35        16.77         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
       10.36         9.93        20.25        19.23        13.32        17.85 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       21.04        18.74         0.13         0.26         2.76         0.03 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L 
       13.55        29.95        71.24        16.47        85.12        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 
       35.24        29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 
       41.42         9.01        56.91        48.49         3.19        32.32 
TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ 
       29.85        23.57        11.77       102.67        70.62        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MU 
       45.57        14.99        11.34        25.28        89.29        25.41 
TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       36.16        34.59        16.96         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2767 
        1.02         0.92         0.99        21.01         0.99         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
        2.01        23.01        19.00         3.02        19.00        12.03 
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-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        4.04        22.98        30.02        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         6.94         8.02        16.18        14.73 
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        89.98 
TCGA-77-7140 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
       20.78        70.13       106.95         0.16        46.78         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       86.76        53.95        37.81        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-A5FZ TCGA-77-A5G1 
        9.63        54.41        65.49        35.90       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
      117.57        22.29         5.92        42.41        42.08        30.81 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       27.62        38.86        12.99        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 
       14.07        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         0.72         7.76        14.63         0.10 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       15.62        25.68        19.33        14.96        24.36        18.18 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       19.73        12.56        16.21        15.85        14.96         0.79 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
       12.39         3.65        24.92         9.50         2.93        11.77 
TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       14.07        20.22         2.70         3.48         4.01         5.26 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        2.30        21.04         0.16         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
       14.14        16.14        17.69        49.87        57.07        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8020 TCGA-98-8021 TCGA-98-8023 
       17.46        19.36        16.57         2.76        30.81        21.34 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
        3.88        18.15        27.02        21.21        20.32        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HF TCGA-NC-A5HH 
       20.71        19.10        12.89        16.11         4.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       45.37        13.74         2.89        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE 
       14.73        83.57        65.49         3.65        16.80         0.43 
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 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.07              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           133.74            174.08 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           18.250            19.165 
[1] "0.1 - 133.7 (18.2)" "0.0 - 174.1 (19.2)"
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         1       16       33        1        14        21
  6P GAIN WILD-TYPE       1       71      118        1        49        71
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  6P GAIN MUTATED           0         15          5        1
  6P GAIN WILD-TYPE         3         47         16        6
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                16                71
  STAGE IB                33               118
  STAGE II                 1                 1
  STAGE IIA               14                49
  STAGE IIB               21                71
  STAGE III                0                 3
  STAGE IIIA              15                47
  STAGE IIIB               5                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    20  68  14   6
  6P GAIN WILD-TYPE  91 222  55  17
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              20                91
  T2              68               222
  T3              14                55
  T4               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                 N0  N1  N2  N3
  6P GAIN MUTATED    74  24   8   1
  6P GAIN WILD-TYPE 238 107  31   4
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              74               238
  N1              24               107
  N2               8                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"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    91   1
  6P GAIN WILD-TYPE 313   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     91    1
  6P GAIN WILD-TYPE  313    6
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              91               313
  1               1                 6
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    26  82
  6P GAIN WILD-TYPE 101 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     26   82
  6P GAIN WILD-TYPE  101  284
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              26               101
  MALE                82               284
[1] 2 2
[1] FALSE
D11V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                       5
  6P GAIN WILD-TYPE                                    10
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                         0
  6P GAIN WILD-TYPE                                       1
                   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                                                         369
D11V9, multiclass
                                                             clus
vv                                                            6P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  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 CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               369
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     3 105
  6P GAIN WILD-TYPE  10 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3  105
  6P GAIN WILD-TYPE   10  375
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                3                10
  YES             105               375
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, continuous
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    88   5   1   4
  6P GAIN WILD-TYPE 306   7   3  18
D11V13, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              88               306
  R1               5                 7
  R2               1                 3
  RX               4                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
  6P GAIN MUTATED       0                        10    77
  6P GAIN WILD-TYPE     9                        21   263
D11V14, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN              10                21
  WHITE                                  77               263
[1] 3 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  69
  6P GAIN WILD-TYPE   6 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2   69
  6P GAIN WILD-TYPE    6  240
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              69               240
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    53  37
  6Q GAIN WILD-TYPE 228 159
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               90               387 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               37               159 
$`6Q GAIN MUTATED`
TCGA-21-1072 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-22-4605 TCGA-22-5477 
       99.16       119.80        43.23        33.93        32.02        44.25 
TCGA-22-5482 TCGA-22-5483 TCGA-33-4533 TCGA-33-4547 TCGA-33-4587 TCGA-33-4589 
       11.74        18.84       133.74        79.53        54.44         1.55 
TCGA-33-AAS8 TCGA-34-7107 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 
       36.62         1.12         7.82         6.81         0.39        44.75 
TCGA-43-2578 TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 TCGA-46-3768 TCGA-46-6026 
       22.49        33.11        27.91        21.47         9.99        13.91 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 
        5.46        30.35         8.75        28.96         2.04         0.62 
TCGA-56-7822 TCGA-56-8308 TCGA-56-A49D TCGA-56-A5DR TCGA-58-8387 TCGA-58-8393 
       17.49        17.00        20.94         0.13        13.25        34.78 
TCGA-58-A46K TCGA-60-2703 TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 TCGA-60-2723 
       34.36        96.82        50.33        35.34        42.64        35.90 
TCGA-60-2725 TCGA-63-A5MH TCGA-63-A5MS TCGA-63-A5MT TCGA-66-2734 TCGA-66-2757 
       26.83        66.61        78.28        16.37        43.10        43.99 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2769 TCGA-66-2777 TCGA-66-2781 TCGA-66-2786 
       25.05         2.01         7.07         2.01         3.98        25.97 
TCGA-66-2789 TCGA-66-2793 TCGA-68-8251 TCGA-77-7142 TCGA-77-7465 TCGA-77-8130 
        4.04        10.06        13.35        42.28        15.75        82.92 
TCGA-85-6798 TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 TCGA-85-8276 TCGA-85-8287 
        6.41        32.91         1.15        18.94        34.52         0.76 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-90-A4EE 
        5.29         3.09        15.62        19.33        17.72        22.62 
TCGA-90-A59Q TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-98-7454 TCGA-98-8022 
       10.59        11.70        14.14        16.14         8.42        30.67 
TCGA-98-A53B TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
        2.01        20.71        13.18        13.41        11.84         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52W TCGA-O2-A5IB 
       64.08        39.85        22.78        83.57         8.58        11.18 

$`6Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       11.34        23.54        92.15        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
       86.96         6.18         2.79       154.32        49.94        27.19 
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-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
       31.73       122.43         9.34        31.63        88.11        41.69 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       10.82        32.19        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
       64.21         1.74        14.10        27.02        48.82        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-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       13.12        19.30         9.57        11.77        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       63.55        14.63         0.79        54.28        71.34        79.20 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
       30.12        62.86        56.32        16.64        22.06         7.63 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6737 
       98.01       174.08       103.53       151.27        14.07        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
       27.02         4.70         0.30         6.94       110.99        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       32.88        31.27        65.23        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       23.24        12.00        16.93        30.94        18.15         4.96 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       27.19         4.04        26.43        20.91         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 
        0.39         6.58         8.12         7.46         3.39        47.80 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
       74.07        68.58        55.20        70.03        60.79         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        27.39        36.39        15.58        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       35.70        17.88        17.06        40.21        38.66        27.02 
TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       18.38        12.36        24.89         5.46         3.81        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        7.76        66.51        13.38        11.77         2.93        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
        9.73        14.20        12.03        10.65         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 
       29.95        28.34        27.45         0.10        18.25         0.99 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
        0.43         0.99         1.45         1.32         0.85         6.51 
TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
        0.10         3.48        26.89        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       15.81        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.26         2.76         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-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
        3.58        12.23        10.22        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
       80.45        49.48        66.54        41.42         9.01        56.91 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 
       48.49         3.19        32.32        29.85        23.57        11.77 
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-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       11.34        25.28        89.29        25.41        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-66-2763 TCGA-66-2766 
        2.01         0.92         0.99        21.01         0.99         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 
        2.01         2.01        23.01        19.00         3.02        19.00 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 
       12.03        12.00        24.95         1.97        40.01        22.98 
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-68-8250 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         6.94         8.02        16.18        14.73 
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        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
       20.78         0.49        70.13       106.95         0.16        46.78 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
        6.51        86.76        53.95        37.81        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         9.63        54.41        65.49        35.90         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       117.57        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       42.08        30.81        27.62        38.86         9.67        11.97 
TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 
       12.99        36.53        34.95        31.30         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        14.07        16.87 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 
       10.09        13.22        22.45        16.77        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        0.72         7.76        14.63        13.94        12.59         0.10 
TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       25.68        14.96        24.36        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96         0.79        12.39         3.65 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
       24.92         9.50         2.93        11.77        14.07        20.22 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
        2.70         3.48         4.01         5.26         2.30        21.04 
TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 
        0.16         4.01         5.03        26.63        17.69        49.87 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8020 
       57.07        18.31        17.46        19.36        16.57         2.76 
TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C 
       30.81        21.34        27.16         3.88        18.15        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
       21.21        20.32        18.58        19.10        12.89        16.11 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        51.78         1.22        45.37        13.74         4.21 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR 
        2.89        37.22        30.58        24.00        14.73        29.75 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       65.49         3.65        16.80         0.43        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       12.72        43.89         0.20 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.07              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           133.74            174.08 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            18.89             19.23 
[1] "0.1 - 133.7 (18.9)" "0.0 - 174.1 (19.2)"
[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        11        14
  6Q GAIN WILD-TYPE       1       72      117        1        52        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  6Q GAIN MUTATED           1         10          5        0
  6Q GAIN WILD-TYPE         2         52         16        7
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                15                72
  STAGE IB                34               117
  STAGE II                 1                 1
  STAGE IIA               11                52
  STAGE IIB               14                78
  STAGE III                1                 2
  STAGE IIIA              10                52
  STAGE IIIB               5                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  56  12   5
  6Q GAIN WILD-TYPE  92 234  57  18
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              19                92
  T2              56               234
  T3              12                57
  T4               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                 N0  N1  N2  N3
  6Q GAIN MUTATED    64  23   3   1
  6Q GAIN WILD-TYPE 248 108  36   4
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              64               248
  N1              23               108
  N2               3                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"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    75   0
  6Q GAIN WILD-TYPE 329   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     75    0
  6Q GAIN WILD-TYPE  329    7
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              75               329
  1               0                 7
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    22  70
  6Q GAIN WILD-TYPE 105 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     22   70
  6Q GAIN WILD-TYPE  105  296
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              22               105
  MALE                70               296
[1] 2 2
[1] FALSE
D12V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED                                       2
  6Q GAIN WILD-TYPE                                    13
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED                                         0
  6Q GAIN WILD-TYPE                                       1
                   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                                                         381
D12V9, multiclass
                                                             clus
vv                                                            6Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  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 CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               381
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  90
  6Q GAIN WILD-TYPE  11 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   90
  6Q GAIN WILD-TYPE   11  390
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                2                11
  YES              90               390
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    72   3   1   4
  6Q GAIN WILD-TYPE 322   9   3  18
D12V13, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              72               322
  R1               3                 9
  R2               1                 3
  RX               4                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
  6Q GAIN MUTATED       0                         6    69
  6Q GAIN WILD-TYPE     9                        25   271
D12V14, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               6                25
  WHITE                                  69               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"
D12V15, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3  61
  6Q GAIN WILD-TYPE   5 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   61
  6Q GAIN WILD-TYPE    5  248
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              61               248
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   143  85
  7P GAIN WILD-TYPE 138 111
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              228               249 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               85               111 
$`7P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        7.46        75.75        79.46       117.57        11.34        23.54 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       36.07        86.96         6.18       154.32        49.94       119.54 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
       99.16        70.16        60.89        31.73         9.34       119.80 
TCGA-21-5783 TCGA-21-5784 TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 
       88.11        41.69         7.33         1.74        14.10        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 
       35.08        24.13         0.56        38.17        13.12        32.02 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       31.73        64.93        63.55        44.25         0.79        54.28 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 
       11.74        18.84        56.32        22.06       133.74        98.01 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-A4WN TCGA-33-AASD 
      174.08       103.53        14.07         1.55         4.70       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 
       44.19        27.16         2.63        28.96        31.27        65.23 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-8456 
       56.38         9.07        12.00        16.93        18.15        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 
       20.91         3.95         0.39         8.12         6.81         0.39 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 
       47.80        74.07        44.75        27.39        15.58        35.70 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       40.21        38.66        27.02        33.11        18.38        27.91 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-A474 TCGA-43-A475 
       24.89         5.46         3.81         7.76        11.61         9.73 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 
       12.03         9.99        10.65         0.39        29.95         5.46 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-8304 TCGA-56-8504 
        0.99         0.99         1.45         0.85         3.48        16.77 
TCGA-56-8624 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DR 
        1.18         9.93        20.94        19.23        13.32         0.13 
TCGA-56-A62T TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N 
        2.76        71.24        16.47        34.78        35.24        29.92 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2711 TCGA-60-2712 
       37.94        92.71        80.45        49.48        41.42         9.01 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 
       56.91        50.33        42.64        29.85        35.90        11.77 
TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR 
      102.67        66.61        58.65        59.97        45.57        89.29 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       16.37        25.41        53.88        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 
        0.99         0.92        25.05         0.99         1.02         2.01 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2782 TCGA-66-2785 
       23.01        19.00         2.01        12.03        12.00         1.97 
TCGA-66-2787 TCGA-66-2791 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 
       40.01         5.03         4.01        49.05         2.73         8.02 
TCGA-68-A59J TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7338 TCGA-77-7463 
       14.73        23.28        11.18        20.78         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       15.75         6.51        86.76        53.95        37.81        82.92 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 
       53.92        39.09       104.09         9.63        54.41         0.33 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
      117.57        22.29         5.92        42.41        42.08        30.81 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       27.62         9.67        12.99         6.41        36.53        34.95 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 
        1.15        29.95        18.94        19.04        24.13        16.87 
TCGA-85-8276 TCGA-85-8352 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN 
       34.52         5.29        32.71         0.10        15.62        19.33 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A513 TCGA-85-A53L TCGA-90-7769 
       18.18        19.73        12.56         0.79        12.39        11.77 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8064 TCGA-94-7557 
       20.22        22.62        10.59         3.48         5.26         0.16 
TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8023 TCGA-98-A53I 
       17.69        57.07        19.36        16.57        21.34        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HE 
       20.71        12.89        16.11        13.41        11.84        64.08 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HP TCGA-NC-A5HR 
       51.78        45.37         2.89        39.85        24.00        29.75 
TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52W 
       83.57         0.43        33.07         3.72        12.72         8.58 

$`7P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 
       12.20         4.80        92.15        31.99         1.64         2.79 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 
       27.19        46.88        34.78        15.58       122.43        43.23 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 
       31.63        33.93        10.82        32.19        21.99        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4601 
        4.31        64.21        27.02        48.82        48.33        34.75 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 
       19.30         9.57        11.77        14.63        71.34        79.20 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 TCGA-33-4583 
       30.12        62.86        16.64         7.63        79.53       151.27 
TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       54.44        19.76        27.02         0.30        36.62         6.94 
TCGA-33-AASJ TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5239 
      118.36        61.61        31.50        32.88        67.79        23.24 
TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-37-3789 
       30.94         4.96         1.12        27.19         4.04         0.43 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 
        6.58         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 
       70.03        60.79         1.71        24.33         1.94        36.39 
TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 TCGA-43-6143 TCGA-43-6770 
       35.64        17.88        17.06        22.49        12.36        21.47 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A56U 
       19.59        66.51        13.38        11.77         2.93        14.20 
TCGA-46-6026 TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
       13.91         0.39        28.34        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 
       28.96         0.10        18.25         2.04         0.62         0.43 
TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 
        1.32         6.51         0.10        17.49        26.89        17.00 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 
       14.07         1.35         1.81        22.75        10.36        20.25 
TCGA-56-8629 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 
       15.81        17.85        21.04        18.74         0.26         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       13.25        13.55        29.95        85.12        34.36        56.65 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 
       21.11         3.58        12.23        10.22        96.82        21.93 
TCGA-60-2710 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
       66.54        35.34        48.49         3.19        32.32        23.57 
TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS 
       26.83        70.62        14.99        11.34        25.28        78.28 
TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
       36.16        34.59        16.96         1.02         2.01         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2773 
       43.99        21.01         2.01         2.01         7.07         3.02 
TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 
       19.00         3.98        24.95        25.97        22.98         4.04 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-68-7756 TCGA-68-7757 
       22.98        30.02        10.06        54.08         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 
       13.35        16.18        29.56        73.12        75.09        89.98 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8131 TCGA-77-8138 
        0.49        42.28        70.13       106.95        12.59        17.72 
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        35.90 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7698 TCGA-85-7699 
      126.18       132.36        38.86        11.97        31.30        32.91 
TCGA-85-7710 TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8287 
        1.38        25.15        31.56        14.07        10.09         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 
       13.22        22.45        16.77         3.09         2.01         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB 
        7.76        14.63        13.94        12.59        25.68        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 
       14.96        24.36        16.21        15.85        14.96         3.65 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-92-7340 TCGA-92-8063 
       24.92         9.50         2.93        14.07         2.70         4.01 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        2.30        21.04        11.70         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 
       14.14        16.14        49.87        18.31        17.46         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
        2.76        30.81        30.67        27.16         3.88        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH TCGA-LA-A446 
        2.01        27.02        21.21        20.32        19.10        13.18 
TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN 
        0.07         4.54         1.22        13.74         4.21        37.22 
TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       30.58        14.73        22.78        65.49         3.65        16.80 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.10              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           174.08            151.27 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           20.845            17.720 
[1] "0.1 - 174.1 (20.8)" "0.0 - 151.3 (17.7)"
[1] "hr=" "1.5"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         2       28       82        0        31        51
  7P GAIN WILD-TYPE       0       59       69        2        32        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  7P GAIN MUTATED           2         29          7        4
  7P GAIN WILD-TYPE         1         33         14        3
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                28                59
  STAGE IB                82                69
  STAGE II                 0                 2
  STAGE IIA               31                32
  STAGE IIB               51                41
  STAGE III                2                 1
  STAGE IIIA              29                33
  STAGE IIIB               7                14
  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    38 159  34   7
  7P GAIN WILD-TYPE  73 131  35  16
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              38                73
  T2             159               131
  T3              34                35
  T4               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                 N0  N1  N2  N3
  7P GAIN MUTATED   143  72  18   2
  7P GAIN WILD-TYPE 169  59  21   3
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             143               169
  N1              72                59
  N2              18                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"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   196   4
  7P GAIN WILD-TYPE 208   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    196    4
  7P GAIN WILD-TYPE  208    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             196               208
  1               4                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    55 183
  7P GAIN WILD-TYPE  72 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     55  183
  7P GAIN WILD-TYPE   72  183
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              55                72
  MALE               183               183
[1] 2 2
[1] FALSE
D13V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED                                       7
  7P GAIN WILD-TYPE                                     8
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED                                         0
  7P GAIN WILD-TYPE                                       1
                   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                                                         240
D13V9, multiclass
                                                             clus
vv                                                            7P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     7
  LUNG CLEAR CELL 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)             230
                                                             clus
vv                                                            7P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               240
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     5 233
  7P GAIN WILD-TYPE   8 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5  233
  7P GAIN WILD-TYPE    8  247
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                5                 8
  YES             233               247
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, continuous
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   194   5   1  10
  7P GAIN WILD-TYPE 200   7   3  12
D13V13, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             194               200
  R1               5                 7
  R2               1                 3
  RX              10                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   152
  7P GAIN WILD-TYPE     1                        14   188
D13V14, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   8                 1
  BLACK OR AFRICAN AMERICAN              17                14
  WHITE                                 152               188
[1] 3 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     2 146
  7P GAIN WILD-TYPE   6 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2  146
  7P GAIN WILD-TYPE    6  163
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO             146               163
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   129  79
  7Q GAIN WILD-TYPE 152 117
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              208               269 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               79               117 
$`7Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        7.46        75.75        79.46       117.57        11.34        23.54 
TCGA-18-3417 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 
       36.07         6.18       154.32       119.54        70.16        60.89 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1081 TCGA-21-5783 TCGA-21-5787 TCGA-21-A5DI 
       34.78        31.73         9.34        88.11        10.82        32.19 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
        1.74        14.10        20.48        35.08        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 TCGA-22-5472 
        0.56        38.17        13.12        32.02        31.73        64.93 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 
       63.55        44.25         0.79        54.28        11.74        18.84 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4586 
       56.32        16.64        22.06       133.74        98.01        14.07 
TCGA-33-4589 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 
        1.55        27.02       110.99        44.19        27.16         2.63 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5236 TCGA-34-5240 
       61.61        28.96        31.27        65.23         9.07        12.00 
TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
       16.93        18.15         1.12        26.43        20.91         3.95 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5027 
        7.82         6.81         0.39        47.80        44.75        60.79 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       27.39        15.58        35.70        27.02        33.11        18.38 
TCGA-43-6647 TCGA-43-6773 TCGA-43-7657 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V 
       24.89         3.81         7.76        11.61         9.73        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
        9.99        10.65         0.39        29.95         5.46        30.35 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-8308 
       18.25         0.99         0.99         1.45         0.85        17.00 
TCGA-56-8504 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 
       16.77        20.94        13.32         0.13         2.76         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-60-2711 TCGA-60-2712 TCGA-60-2713 
       92.71        80.45        49.48        41.42         9.01        56.91 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 TCGA-63-A5MB 
       50.33        42.64        29.85        35.90        11.77       102.67 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MU TCGA-63-A5MW TCGA-66-2734 
       59.97        45.57        89.29        25.41        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-68-8250 TCGA-77-6845 TCGA-77-7141 TCGA-77-7338 
       49.05         2.73         8.02        23.28         0.49         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       46.78        15.75         6.51        53.95        37.81        82.92 
TCGA-77-8133 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
       53.92        26.40         9.63        54.41        65.49         0.33 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       42.41        42.08         9.67        12.99         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        16.87 
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        15.62        19.33 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4ED 
       18.18        19.73        12.56         3.65        11.77        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8169 
       22.62        10.59         3.48        17.69        57.07        18.31 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8023 TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J 
       19.36        16.57        21.34        27.16        18.58        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HE 
       12.89        16.11        13.18        13.41        11.84        64.08 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NK-A5CR 
       51.78        45.37         2.89        24.00        29.75        83.57 
TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52W 
        0.43         3.72        12.72         8.58 

$`7Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 
       12.20         4.80        92.15        31.99         1.64        86.96 
TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1078 
        2.79        49.94        27.19        46.88        99.16        15.58 
TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
      122.43       119.80        43.23        31.63        41.69        33.93 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 
       21.99         7.33        14.93         4.31        64.21        27.02 
TCGA-22-1017 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 
       48.82        34.75        19.30         9.57        11.77        14.63 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-33-4532 TCGA-33-4547 
       71.34        79.20        30.12        62.86         7.63        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6737 TCGA-33-A4WN 
      174.08       103.53       151.27        54.44        19.76         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2604 TCGA-34-2608 
        0.30        36.62         6.94       118.36        31.50        32.88 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       67.79        56.38        23.24        30.94         4.96        27.19 
TCGA-34-8455 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        4.04         0.43         0.39         6.58         8.12         7.46 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
        3.39        74.07        68.58        55.20        70.03         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 
       24.33         1.94        36.39        35.64        17.88        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 
       40.21        22.49        38.66        27.91        12.36        21.47 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        5.46        19.59        66.51        13.38        11.77         2.93 
TCGA-43-A56U TCGA-46-6026 TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 
       14.20        13.91         0.39        28.34         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7580 
       28.96         0.10         2.04         0.62         0.43         1.32 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        6.51         0.10        17.49         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         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.25        15.81        19.23        17.85        21.04        18.74 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
        0.26        13.25        13.55        29.95        71.24        85.12 
TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       56.65        21.11         3.58        12.23        10.22        96.82 
TCGA-60-2707 TCGA-60-2710 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 
       21.93        66.54        35.34        48.49         3.19        32.32 
TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM 
       23.57        26.83        70.62        66.61        58.65        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-66-2727 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 
       16.96         0.99         1.02         2.01         0.99        43.99 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 
       25.05         2.01         2.01         7.07         3.02        19.00 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        3.98        24.95        25.97        22.98         4.04        22.98 
TCGA-66-2793 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       10.06         6.64         6.94        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 
       29.56        73.12        75.09        11.18        89.98        20.78 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 
       42.28        70.13       106.95        86.76        12.59        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 
       17.72       104.09        11.54        27.39         6.97        35.90 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GB 
      126.18       132.36       117.57        22.29         5.92        30.81 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       27.62        38.86        11.97        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        14.07         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         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB 
       14.63        13.94        12.59         0.10        25.68        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       14.96        24.36        16.21        15.85        14.96         0.79 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-92-7340 
       12.39        24.92         9.50         2.93        14.07         2.70 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        4.01         5.26         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 
        4.01         5.03        26.63        14.14        16.14        49.87 
TCGA-96-8170 TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-A539 
       17.46         8.42         2.76        30.81        30.67         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH 
       18.15         2.01        27.02        21.21        20.32        19.10 
TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM 
        0.07         4.54         1.22        13.74         4.21        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX 
       37.22        30.58        14.73        22.78        65.49         3.65 
TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       16.80        33.07        43.89        11.18         0.20 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           154.32            174.08 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            20.35             17.88 
[1] "0.0 - 154.3 (20.4)" "0.1 - 174.1 (17.9)"
[1] "hr=" "1.2"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         1       26       69        1        27        46
  7Q GAIN WILD-TYPE       1       61       82        1        36        46
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  7Q GAIN MUTATED           2         30          9        5
  7Q GAIN WILD-TYPE         1         32         12        2
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                26                61
  STAGE IB                69                82
  STAGE II                 1                 1
  STAGE IIA               27                36
  STAGE IIB               46                46
  STAGE III                2                 1
  STAGE IIIA              30                32
  STAGE IIIB               9                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
  7Q GAIN MUTATED    37 138  34   9
  7Q GAIN WILD-TYPE  74 152  35  14
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              37                74
  T2             138               152
  T3              34                35
  T4               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                 N0  N1  N2  N3
  7Q GAIN MUTATED   127  67  20   2
  7Q GAIN WILD-TYPE 185  64  19   3
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             127               185
  N1              67                64
  N2              20                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"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   180   5
  7Q GAIN WILD-TYPE 224   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    180    5
  7Q GAIN WILD-TYPE  224    2
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             180               224
  1               5                 2
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    50 168
  7Q GAIN WILD-TYPE  77 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     50  168
  7Q GAIN WILD-TYPE   77  198
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              50                77
  MALE               168               198
[1] 2 2
[1] FALSE
D14V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                       7
  7Q GAIN WILD-TYPE                                     8
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                         0
  7Q GAIN WILD-TYPE                                       1
                   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                                                           210
  7Q GAIN WILD-TYPE                                                         260
D14V9, multiclass
                                                             clus
vv                                                            7Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     7
  LUNG CLEAR CELL 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)             210
                                                             clus
vv                                                            7Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               260
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     5 213
  7Q GAIN WILD-TYPE   8 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  213
  7Q GAIN WILD-TYPE    8  267
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                5                 8
  YES             213               267
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   174   6   1   8
  7Q GAIN WILD-TYPE 220   6   3  14
D14V13, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             174               220
  R1               6                 6
  R2               1                 3
  RX               8                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
  7Q GAIN MUTATED       6                        17   141
  7Q GAIN WILD-TYPE     3                        14   199
D14V14, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   6                 3
  BLACK OR AFRICAN AMERICAN              17                14
  WHITE                                 141               199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 136
  7Q GAIN WILD-TYPE   6 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  136
  7Q GAIN WILD-TYPE    6  173
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO             136               173
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    72  53
  8P GAIN WILD-TYPE 209 143
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              125               352 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               53               143 
$`8P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3416 
        7.46        79.46         4.80       117.57        23.54        31.99 
TCGA-18-3421 TCGA-21-1070 TCGA-21-1075 TCGA-21-1079 TCGA-21-1082 TCGA-21-5783 
       86.96       119.54        70.16        31.73       119.80        88.11 
TCGA-21-5784 TCGA-22-1011 TCGA-22-4596 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
       41.69         1.74         0.56        64.93        63.55        14.63 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       54.28        11.74        62.86        22.06         7.63       133.74 
TCGA-33-4583 TCGA-33-4587 TCGA-33-6737 TCGA-33-AASB TCGA-34-2605 TCGA-34-5231 
      151.27        54.44        19.76         6.94        28.96        65.23 
TCGA-34-5232 TCGA-34-5239 TCGA-34-7107 TCGA-34-A5IX TCGA-37-4132 TCGA-37-5819 
       67.79        23.24         1.12        20.91         7.46         3.39 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5034 
       44.75        55.20        70.03         1.71        24.33        36.39 
TCGA-39-5040 TCGA-43-2578 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-A56V 
       17.06        22.49        33.11        27.91        24.89        12.03 
TCGA-52-7811 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-A49D TCGA-56-A4ZK 
        8.75         6.51         0.10         3.48        20.94        18.74 
TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-60-2695 TCGA-60-2708 TCGA-60-2712 
        0.13         2.76         0.03        21.11        80.45         9.01 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 TCGA-63-A5MG 
       50.33        42.64         3.19        29.85        26.83        70.62 
TCGA-63-A5MH TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MY TCGA-66-2742 TCGA-66-2744 
       66.61        45.57        89.29        34.59        21.07         0.99 
TCGA-66-2756 TCGA-66-2763 TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
        0.99         0.99         2.01        23.01         3.02         2.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 
       22.98         4.04        10.06        49.05         6.64        13.35 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7463 TCGA-77-8007 TCGA-77-8136 
       89.98         0.49        70.13        46.78         6.51        39.09 
TCGA-77-8138 TCGA-77-8143 TCGA-77-8150 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6560 
       17.72        26.40        54.41         5.92        38.86        11.97 
TCGA-85-7699 TCGA-85-8052 TCGA-85-8287 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       32.91        24.13         0.76         7.76        14.63        13.94 
TCGA-85-8664 TCGA-85-A510 TCGA-85-A513 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 
        0.10        15.85         0.79        11.77        22.62         2.70 
TCGA-94-7943 TCGA-96-7545 TCGA-96-8169 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B 
       11.70        57.07        18.31        21.34        18.15         2.01 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HK TCGA-NC-A5HM 
       12.89        16.11        13.41         0.07         4.21        39.85 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52W TCGA-XC-AA0X 
       83.57         3.65         0.43         8.58         0.20 

$`8P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
       12.20        75.75        11.34        92.15        36.07         1.64 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
        6.18         2.79       154.32        49.94        27.19        46.88 
TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
       99.16        60.89        34.78        15.58       122.43         9.34 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
       43.23        31.63        33.93        10.82        32.19        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 
        7.33        14.93         4.31        64.21        14.10        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
       48.82        20.48        35.08        48.33        24.13        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-22-5471 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 
       31.73        44.25         0.79        71.34        79.20        18.84 
TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       30.12        56.32        16.64        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
      103.53        14.07         1.55        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
       36.62       110.99        44.19       118.36        27.16         2.63 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5234 TCGA-34-5236 
       61.61        31.50        32.88        31.27        56.38         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 
       12.00        16.93        30.94        18.15         4.96        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
        4.04        26.43         3.95         0.43         0.39         6.58 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 
        8.12         7.82         6.81         0.39        47.80        74.07 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
       68.58        60.79         1.94        27.39        15.58        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 
       35.70        17.88        40.21        38.66        27.02        18.38 
TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
       12.36        21.47         5.46         3.81        19.59         7.76 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
       66.51        13.38        11.77         2.93        11.61         9.73 
TCGA-43-A56U TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       14.20         9.99        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-56-6546 TCGA-56-7221 TCGA-56-7222 
        0.10        18.25         2.04         0.62         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-8307 
        0.99         1.45         1.32         0.85        17.49        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
       17.00        14.07         1.35        16.77         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
        1.18        10.36         9.93        20.25        15.81        19.23 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 
       13.32        17.85        21.04         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-60-2696 TCGA-60-2697 TCGA-60-2698 
       56.65        35.24        29.92         3.58        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
       96.82        37.94        92.71        21.93        49.48        66.54 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 TCGA-60-2723 
       41.42        56.91        35.34        48.49        32.32        35.90 
TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM 
       23.57        11.77       102.67        58.65        59.97        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV 
       11.34        25.28        78.28        16.37        25.41        36.16 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 
       53.88        16.96        43.10         2.01         1.02         2.01 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
        0.92        43.99        21.01        25.05         2.01         1.02 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        2.01         7.07        19.00        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 
       12.00        24.95         1.97        25.97        40.01        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 
        5.03        30.02        54.08         4.01         2.73         6.94 
TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
        8.02        16.18        14.73        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 
       23.28        11.18        20.78        42.28       106.95         0.16 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
       15.75        86.76        53.95        37.81        82.92        12.59 
TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       53.92       104.09        11.54        27.39         6.97         9.63 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       65.49        35.90         0.33       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6175 
       22.29        42.41        42.08        30.81        27.62         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
       12.99         6.41        36.53        34.95        31.30         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 
        1.15        29.95        18.94        25.15        19.04        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 
       14.07        16.87        34.52        10.09        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         0.72 
TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
       12.59        15.62        25.68        19.33        17.72        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
       24.36        18.18        19.73        12.56        16.21        14.96 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 
       12.39         3.65        24.92         9.50         2.93        14.07 
TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       20.22        10.59         3.48         4.01         5.26         2.30 
TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
       21.04         0.16         4.01         5.03        26.63        14.14 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       16.14        17.69        49.87        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 
        8.42         2.76        30.81        30.67        27.16         3.88 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       27.02        21.21        20.32        18.58        20.71        19.10 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       13.18        11.84        64.08         4.54        51.78         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       45.37        13.74         2.89        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N 
       14.73        29.75        22.78        65.49        16.80        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
        3.72        12.72        43.89        11.18 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.03              0.10 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           151.27            174.08 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            20.91             19.02 
[1] "0.0 - 151.3 (20.9)" "0.1 - 174.1 (19.0)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         1       17       45        1        11        21
  8P GAIN WILD-TYPE       1       70      106        1        52        71
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  8P GAIN MUTATED           0         18          9        4
  8P GAIN WILD-TYPE         3         44         12        3
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                17                70
  STAGE IB                45               106
  STAGE II                 1                 1
  STAGE IIA               11                52
  STAGE IIB               21                71
  STAGE III                0                 3
  STAGE IIIA              18                44
  STAGE IIIB               9                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
  8P GAIN MUTATED    25  77  15  11
  8P GAIN WILD-TYPE  86 213  54  12
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              25                86
  T2              77               213
  T3              15                54
  T4              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                 N0  N1  N2  N3
  8P GAIN MUTATED    84  28  11   2
  8P GAIN WILD-TYPE 228 103  28   3
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              84               228
  N1              28               103
  N2              11                28
  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 298   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    106    4
  8P GAIN WILD-TYPE  298    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             106               298
  1               4                 3
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    33  95
  8P GAIN WILD-TYPE  94 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     33   95
  8P GAIN WILD-TYPE   94  271
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              33                94
  MALE                95               271
[1] 2 2
[1] FALSE
D15V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                       2
  8P GAIN WILD-TYPE                                    13
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                         0
  8P GAIN WILD-TYPE                                       1
                   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                                                           124
  8P GAIN WILD-TYPE                                                         346
D15V9, multiclass
                                                             clus
vv                                                            8P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             124
                                                             clus
vv                                                            8P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               346
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     4 124
  8P GAIN WILD-TYPE   9 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4  124
  8P GAIN WILD-TYPE    9  356
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                4                 9
  YES             124               356
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, continuous
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED   105   4   0   1
  8P GAIN WILD-TYPE 289   8   4  21
D15V13, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0             105               289
  R1               4                 8
  R2               0                 4
  RX               1                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
  8P GAIN MUTATED       3                        11    81
  8P GAIN WILD-TYPE     6                        20   259
D15V14, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              11                20
  WHITE                                  81               259
[1] 3 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  78
  8P GAIN WILD-TYPE   5 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   78
  8P GAIN WILD-TYPE    5  231
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              78               231
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   140 108
  8Q GAIN WILD-TYPE 141  88
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              248               229 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              108                88 
$`8Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        7.46        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-5595 
       31.99        36.07         1.64        86.96         6.18        27.19 
TCGA-21-1070 TCGA-21-1075 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
      119.54        70.16        31.73         9.34       119.80        43.23 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1011 
       88.11        41.69        33.93        10.82        32.19         1.74 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4596 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 
       27.02        48.82         0.56        32.02         9.57        11.77 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       64.93        63.55        14.63        44.25         0.79        54.28 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4532 
       79.20        11.74        30.12        62.86        22.06         7.63 
TCGA-33-4533 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-AASB 
      133.74       151.27        54.44         1.55        19.76         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
      110.99        44.19        28.96        31.27        65.23        67.79 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX 
       23.24        16.93        18.15        27.19         4.04        20.91 
TCGA-37-3789 TCGA-37-4132 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 
        0.43         7.46         3.39        74.07        44.75        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 
       70.03         1.71        24.33        36.39        15.58        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       40.21        22.49        38.66        33.11        18.38        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-7657 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56V 
       24.89        21.47         7.76         2.93         9.73        12.03 
TCGA-46-3768 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
        9.99        30.35         8.75        28.96         0.10         2.04 
TCGA-56-6546 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8504 
        0.62         0.10        17.49         3.48        17.00        16.77 
TCGA-56-8622 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DR 
        1.81        20.25        20.94        13.32        18.74         0.13 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8392 TCGA-58-8393 
        0.26         2.76         0.03        13.25        16.47        34.78 
TCGA-58-A46J TCGA-58-A46M TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       85.12        35.24        21.11        10.22        96.82        37.94 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
       21.93        80.45         9.01        56.91        50.33        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-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR 
       70.62        66.61        58.65        59.97        45.57        89.29 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       53.88        34.59        43.10        21.07         0.99         1.02 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2767 TCGA-66-2769 
        0.92         0.99        43.99         0.99         2.01         7.07 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2782 TCGA-66-2788 TCGA-66-2789 
       23.01         3.02         2.01        12.00        22.98         4.04 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 
       22.98        30.02        10.06        49.05         6.64        13.35 
TCGA-68-A59I TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       16.18        75.09        89.98         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        15.75         6.51        53.95        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       82.92        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G6 TCGA-77-A5G7 
       11.54        26.40         9.63        54.41        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7699 
       42.41        38.86         9.67        11.97         6.41        32.91 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8287 TCGA-85-8350 
        1.15        18.94        24.13        31.56         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        14.63        13.94        12.59         0.10 
TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
       15.62        17.72        14.96        18.18        19.73        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
       14.96         0.79         3.65         2.93        11.77        22.62 
TCGA-92-7340 TCGA-92-7341 TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I4 
        2.70         3.48         0.16        11.70        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8020 
       17.69        57.07        18.31        17.46        19.36         2.76 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
       30.67        21.34        27.16         3.88        18.15         2.01 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF 
       19.10        12.89        16.11        13.41         0.07         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HQ TCGA-NC-A5HR 
       51.78         1.22         4.21        39.85        14.73        29.75 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       22.78        83.57         3.65         0.43        33.07         3.72 
TCGA-O2-A52W TCGA-XC-AA0X 
        8.58         0.20 

$`8Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3415 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       12.20        75.75        92.15         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-21-5782 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       31.63        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
       14.10        20.48        35.08        48.33        24.13        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-5471 TCGA-22-5480 TCGA-22-5483 
       34.75        13.12        19.30        31.73        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        98.01        79.53       174.08       103.53 
TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ 
       14.07        27.02         4.70         0.30        36.62       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5234 
       27.16         2.63        61.61        31.50        32.88        56.38 
TCGA-34-5236 TCGA-34-5240 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 
        9.07        12.00        30.94         4.96         1.12        26.43 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 
        3.95         0.39         6.58         8.12         7.82         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 TCGA-39-5027 TCGA-39-5030 TCGA-39-5031 
        0.39        47.80        68.58        60.79         1.94        27.39 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-3394 TCGA-43-6143 TCGA-43-6771 
       35.64        35.70        17.88        27.02        12.36         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 
        3.81        19.59        66.51        13.38        11.77        11.61 
TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       14.20        10.65        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 
       28.34         5.46        27.45        18.25         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-8307 
        0.99         1.45         1.32         0.85         6.51        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       14.07         1.35        22.75         1.18        10.36         9.93 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-58-8388 TCGA-58-8390 
       15.81        19.23        17.85        21.04        13.55        29.95 
TCGA-58-8391 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 
       71.24        34.36        56.65        29.92         3.58        12.23 
TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 
       92.71        49.48        66.54        41.42        35.34        48.49 
TCGA-60-2721 TCGA-63-A5MB TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS 
       32.32       102.67        14.99        11.34        25.28        78.28 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-66-2727 TCGA-66-2737 TCGA-66-2754 
       16.37        25.41        36.16        16.96         2.01         2.01 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 
       21.01        25.05         2.01         1.02         2.01        19.00 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       19.00        12.03         3.98        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 
       40.01         5.03        54.08         4.01         2.73         6.94 
TCGA-68-8250 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 
        8.02        14.73        29.56        73.12        23.28        11.18 
TCGA-77-7140 TCGA-77-7142 TCGA-77-8008 TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 
       20.78        42.28        86.76        27.39         6.97        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GA 
       35.90         0.33       126.18       132.36       117.57        42.08 
TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       30.81        27.62        12.99        36.53        34.95        31.30 
TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 
        1.38        29.95        25.15        19.04        14.07        16.87 
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         0.72        25.68        19.33        24.36        12.56 
TCGA-85-A50Z TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED 
       16.21        12.39        24.92         9.50        14.07        20.22 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 
       10.59         4.01         5.26         2.30        21.04         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
        5.03        26.63        49.87        16.57         8.42        30.81 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-LA-A446 
       27.02        21.21        20.32        18.58        20.71        13.18 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN 
       11.84        64.08        45.37        13.74         2.89        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52S TCGA-O2-A52V 
       30.58        24.00        65.49        16.80        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 
           151.27            174.08 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            18.56             19.33 
[1] "0.0 - 151.3 (18.6)" "0.3 - 174.1 (19.3)"
[1] "hr=" "1.2"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         2       36       79        0        27        55
  8Q GAIN WILD-TYPE       0       51       72        2        36        37
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  8Q GAIN MUTATED           1         37         11        6
  8Q GAIN WILD-TYPE         2         25         10        1
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                36                51
  STAGE IB                79                72
  STAGE II                 0                 2
  STAGE IIA               27                36
  STAGE IIB               55                37
  STAGE III                1                 2
  STAGE IIIA              37                25
  STAGE IIIB              11                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
  8Q GAIN MUTATED    47 154  40  14
  8Q GAIN WILD-TYPE  64 136  29   9
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              47                64
  T2             154               136
  T3              40                29
  T4              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                 N0  N1  N2  N3
  8Q GAIN MUTATED   155  75  19   2
  8Q GAIN WILD-TYPE 157  56  20   3
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             155               157
  N1              75                56
  N2              19                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"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   211   6
  8Q GAIN WILD-TYPE 193   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    211    6
  8Q GAIN WILD-TYPE  193    1
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             211               193
  1               6                 1
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    65 190
  8Q GAIN WILD-TYPE  62 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     65  190
  8Q GAIN WILD-TYPE   62  176
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              65                62
  MALE               190               176
[1] 2 2
[1] FALSE
D16V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                       6
  8Q GAIN WILD-TYPE                                     9
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                         0
  8Q GAIN WILD-TYPE                                       1
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  8Q GAIN MUTATED                                        3
  8Q GAIN WILD-TYPE                                      3
                   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                                                           245
  8Q GAIN WILD-TYPE                                                         225
D16V9, multiclass
                                                             clus
vv                                                            8Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             245
                                                             clus
vv                                                            8Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               225
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     8 247
  8Q GAIN WILD-TYPE   5 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      8  247
  8Q GAIN WILD-TYPE    5  233
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                8                 5
  YES             247               233
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   205   7   0  11
  8Q GAIN WILD-TYPE 189   5   4  11
D16V13, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             205               189
  R1               7                 5
  R2               0                 4
  RX              11                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
  8Q GAIN MUTATED       5                        21   169
  8Q GAIN WILD-TYPE     4                        10   171
D16V14, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   5                 4
  BLACK OR AFRICAN AMERICAN              21                10
  WHITE                                 169               171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     5 159
  8Q GAIN WILD-TYPE   3 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5  159
  8Q GAIN WILD-TYPE    3  150
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             159               150
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    34  27
  9P GAIN WILD-TYPE 247 169
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               61               416 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               27               169 
$`9P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-22-4604 TCGA-22-5481 TCGA-33-4532 
        7.46         4.80        31.99        13.12        79.20         7.63 
TCGA-33-4533 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-AASJ 
      133.74       174.08       151.27        14.07         1.55       118.36 
TCGA-34-5239 TCGA-34-5240 TCGA-34-7107 TCGA-37-3792 TCGA-37-4133 TCGA-39-5030 
       23.24        12.00         1.12         0.39         7.82         1.94 
TCGA-39-5036 TCGA-43-6143 TCGA-43-7658 TCGA-43-A475 TCGA-46-6025 TCGA-51-4079 
       35.64        12.36        66.51         9.73        10.65         0.39 
TCGA-52-7622 TCGA-56-8308 TCGA-58-8386 TCGA-60-2695 TCGA-60-2704 TCGA-60-2712 
       28.34        17.00         0.03        21.11        37.94         9.01 
TCGA-60-2714 TCGA-60-2722 TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MU 
       50.33        29.85        59.97        45.57        25.28        25.41 
TCGA-66-2756 TCGA-68-7755 TCGA-68-8250 TCGA-77-8007 TCGA-77-8133 TCGA-77-8136 
        0.99         2.73         8.02         6.51        53.92        39.09 
TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-7698 
       54.41       117.57        42.08        27.62        12.99        31.30 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8353 TCGA-92-8064 TCGA-94-A5I4 
       31.56        16.87        10.09         3.09         5.26        16.14 
TCGA-98-A53I TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HR 
       18.58        13.74         2.89        39.85        37.22        29.75 
TCGA-XC-AA0X 
        0.20 

$`9P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20        75.75        79.46       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       92.15        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
      154.32        49.94        27.19       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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       33.93        10.82        32.19        21.99         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
        4.31        64.21         1.74        14.10        27.02        48.82 
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-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       34.75        32.02        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       64.93        63.55        14.63        44.25         0.79        54.28 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       71.34        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4587 
       16.64        22.06        98.01        79.53       103.53        54.44 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       19.76        27.02         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
      110.99        44.19        27.16         2.63        61.61        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       28.96        32.88        31.27        65.23        67.79        56.38 
TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 
        9.07        16.93        30.94        18.15         4.96        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
        4.04        26.43        20.91         3.95         0.43         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        8.12         7.46         6.81         0.39         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       74.07        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 
        1.71        24.33        27.39        36.39        15.58        35.70 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
       17.88        17.06        40.21        22.49        38.66        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       33.11        18.38        27.91        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        3.81        19.59         7.76        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4080 
       11.61        14.20        12.03         9.99        13.91         0.39 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
       29.95         5.46        30.35         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        0.10        18.25         2.04         0.62         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.99         1.45         1.32         0.85         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
       17.49         3.48        26.89        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
       15.81        20.94        19.23        13.32        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 
       18.74         0.13         0.26         2.76        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-60-2696 TCGA-60-2697 TCGA-60-2698 
       56.65        35.24        29.92         3.58        12.23        10.22 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       96.82        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       41.42        56.91        35.34        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       32.32        35.90        23.57        26.83        11.77       102.67 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR 
       70.62        66.61        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-66-2744 TCGA-66-2753 TCGA-66-2754 
       43.10         2.01        21.07         0.99         1.02         2.01 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.92        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-66-2773 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-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         5.03        30.02        10.06        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-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        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       20.78         0.49        42.28        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        15.75        86.76        53.95        37.81        82.92 
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         9.63        65.49        35.90         0.33       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH 
      132.36        22.29         5.92        42.41        30.81        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
        9.67        11.97         6.41        36.53        34.95        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-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       24.13        14.07        34.52         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         5.29        32.71         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       19.33        17.72        14.96        24.36        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       12.56        16.21        15.85        14.96         0.79        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
        3.65        24.92         9.50         2.93        11.77        14.07 
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-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.30        21.04         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
       26.63        14.14        17.69        49.87        57.07        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 
       17.46        19.36        16.57         8.42         2.76        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
       30.67        21.34        27.16         3.88        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       27.02        21.21        20.32        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       16.11        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HO 
        4.54        51.78         1.22        45.37         4.21        30.58 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       24.00        14.73        22.78        83.57        65.49         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       16.80         0.43        33.07         3.72        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB 
        8.58        11.18 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.03              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           174.08            154.32 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           17.000            19.265 
[1] "0.0 - 174.1 (17.0)" "0.1 - 154.3 (19.3)"
[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       16        1         9        18
  9P GAIN WILD-TYPE       2       80      135        1        54        74
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  9P GAIN MUTATED           0          6          3        1
  9P GAIN WILD-TYPE         3         56         18        6
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 7                80
  STAGE IB                16               135
  STAGE II                 1                 1
  STAGE IIA                9                54
  STAGE IIB               18                74
  STAGE III                0                 3
  STAGE IIIA               6                56
  STAGE IIIB               3                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
  9P GAIN MUTATED     9  41   8   3
  9P GAIN WILD-TYPE 102 249  61  20
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               9               102
  T2              41               249
  T3               8                61
  T4               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                 N0  N1  N2  N3
  9P GAIN MUTATED    31  26   2   0
  9P GAIN WILD-TYPE 281 105  37   5
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              31               281
  N1              26               105
  N2               2                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"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    54   1
  9P GAIN WILD-TYPE 350   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     54    1
  9P GAIN WILD-TYPE  350    6
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              54               350
  1               1                 6
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    16  45
  9P GAIN WILD-TYPE 111 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     16   45
  9P GAIN WILD-TYPE  111  321
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              16               111
  MALE                45               321
[1] 2 2
[1] FALSE
D17V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED                                       4
  9P GAIN WILD-TYPE                                    11
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED                                         0
  9P GAIN WILD-TYPE                                       1
                   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                                                            57
  9P GAIN WILD-TYPE                                                         413
D17V9, multiclass
                                                             clus
vv                                                            9P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG CLEAR CELL 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)              57
                                                             clus
vv                                                            9P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               413
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  60
  9P GAIN WILD-TYPE  12 420
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   60
  9P GAIN WILD-TYPE   12  420
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                12
  YES              60               420
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, continuous
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    48   2   0   3
  9P GAIN WILD-TYPE 346  10   4  19
D17V13, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              48               346
  R1               2                10
  R2               0                 4
  RX               3                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    39
  9P GAIN WILD-TYPE     7                        26   301
D17V14, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               5                26
  WHITE                                  39               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"
D17V15, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  34
  9P GAIN WILD-TYPE   6 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   34
  9P GAIN WILD-TYPE    6  275
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              34               275
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    53  38
  9Q GAIN WILD-TYPE 228 158
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               91               386 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               38               158 
$`9Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3412 TCGA-18-3416 TCGA-21-1072 TCGA-21-1076 
        7.46         4.80        11.34        31.99        99.16        60.89 
TCGA-22-0940 TCGA-22-0944 TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5477 
       21.99         7.33        38.17        13.12        11.77        44.25 
TCGA-22-5483 TCGA-33-4533 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 
       18.84       133.74       174.08       151.27        14.07         1.55 
TCGA-33-AASJ TCGA-34-2596 TCGA-34-5239 TCGA-34-7107 TCGA-37-3792 TCGA-37-4133 
      118.36         2.63        23.24         1.12         0.39         7.82 
TCGA-39-5030 TCGA-39-5036 TCGA-43-3394 TCGA-43-5668 TCGA-43-6143 TCGA-43-7658 
        1.94        35.64        27.02        18.38        12.36        66.51 
TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-52-7622 TCGA-52-7809 
        9.73         9.99        10.65         0.39        28.34         5.46 
TCGA-56-7582 TCGA-56-8308 TCGA-56-A4BX TCGA-58-8386 TCGA-58-8391 TCGA-58-A46M 
        0.85        17.00        13.32         0.03        71.24        35.24 
TCGA-60-2695 TCGA-60-2704 TCGA-60-2710 TCGA-60-2711 TCGA-60-2722 TCGA-63-A5MJ 
       21.11        37.94        66.54        41.42        29.85        59.97 
TCGA-63-A5ML TCGA-63-A5MP TCGA-66-2744 TCGA-66-2756 TCGA-66-2757 TCGA-66-2770 
       45.57        25.28         0.99         0.99        43.99        23.01 
TCGA-66-2792 TCGA-68-7755 TCGA-77-7141 TCGA-77-7335 TCGA-77-7465 TCGA-77-8009 
       30.02         2.73         0.49        70.13        15.75        53.95 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 
       53.92        39.09        27.39        54.41        65.49       117.57 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-7696 TCGA-85-7698 TCGA-85-7844 TCGA-85-8070 
       42.08        27.62        36.53        31.30        29.95        31.56 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8353 TCGA-85-8580 TCGA-85-A4CN TCGA-85-A5B5 
       16.87        10.09         3.09        14.63        19.33         3.65 
TCGA-90-7769 TCGA-94-A5I4 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-A53I TCGA-98-A53J 
       11.77        16.14        19.36        16.57        18.58        20.71 
TCGA-L3-A524 TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HR TCGA-NK-A5CR TCGA-O2-A52N 
       16.11        13.74         2.89        29.75        83.57        33.07 
TCGA-XC-AA0X 
        0.20 

$`9Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
       12.20        75.75        79.46       117.57        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       36.07         1.64        86.96         6.18         2.79       154.32 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 
       49.94        27.19       119.54        46.88        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-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
       31.63        88.11        41.69        33.93        10.82        32.19 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         4.31        64.21         1.74        14.10        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       48.82        20.48        35.08        48.33        24.13         0.56 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 
       34.75        32.02        19.30         9.57        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       63.55        14.63         0.79        54.28        71.34        79.20 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       11.74        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4587 TCGA-33-6737 
        7.63        98.01        79.53       103.53        54.44        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       27.02         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       44.19        27.16        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 
       31.27        65.23        67.79        56.38         9.07        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 
       16.93        30.94        18.15         4.96        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
       26.43        20.91         3.95         0.43         6.58         8.12 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
        7.46         6.81         0.39         3.39        47.80        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
       44.75        68.58        55.20        70.03        60.79         1.71 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 
       24.33        27.39        36.39        15.58        35.70        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 
       17.06        40.21        22.49        38.66        33.11        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
       24.89        21.47         5.46         3.81        19.59         7.76 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
       13.38        11.77         2.93        11.61        14.20        12.03 
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-56-6546 TCGA-56-7221 
       28.96         0.10        18.25         2.04         0.62         0.99 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
        0.43         0.99         1.45         1.32         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
       17.49         3.48        26.89        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       15.81        20.94        19.23        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.13         0.26         2.76        13.25        13.55        29.95 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46N 
       16.47        34.78        85.12        34.36        56.65        29.92 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
        3.58        12.23        10.22        96.82        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       80.45        49.48         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
       48.49        42.64         3.19        32.32        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       26.83        11.77       102.67        70.62        66.61        58.65 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       14.99        11.34        89.29        78.28        16.37        25.41 
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-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2758 TCGA-66-2759 
       21.07         1.02         2.01         0.92        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-66-2777 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-66-2793 TCGA-66-2794 TCGA-66-2795 
        4.04        22.98         5.03        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
       49.05         6.64         6.94         8.02        13.35        16.18 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       14.73        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
       89.98        20.78        42.28       106.95         0.16        46.78 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 
        6.51        86.76        37.81        82.92        12.59        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         9.63        35.90 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        0.33       126.18       132.36        22.29         5.92        42.41 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
       30.81        38.86         9.67        11.97        12.99         6.41 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 
       34.95        32.91         1.38         1.15        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
       19.04        24.13        14.07        34.52         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       22.45        16.77         5.29        32.71         2.01         0.72 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
        7.76        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       17.72        14.96        24.36        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       16.21        15.85        14.96         0.79        12.39        24.92 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        9.50         2.93        14.07        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
        2.70         3.48         4.01         5.26         2.30        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        0.16        11.70         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 
       17.69        49.87        57.07        18.31        17.46         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH 
       18.15         2.01        27.02        21.21        20.32        19.10 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       12.89        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM 
        4.54        51.78         1.22        45.37         4.21        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CT 
       37.22        30.58        24.00        14.73        22.78        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
        3.65        16.80         0.43         3.72        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB 
        8.58        11.18 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.03              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           174.08            154.32 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            20.71             19.00 
[1] "0.0 - 174.1 (20.7)" "0.1 - 154.3 (19.0)"
[1] "hr=" "1.1"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         1       11       29        1        16        20
  9Q GAIN WILD-TYPE       1       76      122        1        47        72
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  9Q GAIN MUTATED           0          8          4        1
  9Q GAIN WILD-TYPE         3         54         17        6
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                11                76
  STAGE IB                29               122
  STAGE II                 1                 1
  STAGE IIA               16                47
  STAGE IIB               20                72
  STAGE III                0                 3
  STAGE IIIA               8                54
  STAGE IIIB               4                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
  9Q GAIN MUTATED    17  60  10   4
  9Q GAIN WILD-TYPE  94 230  59  19
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              17                94
  T2              60               230
  T3              10                59
  T4               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                 N0  N1  N2  N3
  9Q GAIN MUTATED    52  34   4   0
  9Q GAIN WILD-TYPE 260  97  35   5
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              52               260
  N1              34                97
  N2               4                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"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    82   1
  9Q GAIN WILD-TYPE 322   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     82    1
  9Q GAIN WILD-TYPE  322    6
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              82               322
  1               1                 6
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    25  66
  9Q GAIN WILD-TYPE 102 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     25   66
  9Q GAIN WILD-TYPE  102  300
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              25               102
  MALE                66               300
[1] 2 2
[1] FALSE
D18V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED                                       4
  9Q GAIN WILD-TYPE                                    11
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED                                         0
  9Q GAIN WILD-TYPE                                       1
                   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                                                         383
D18V9, multiclass
                                                             clus
vv                                                            9Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG CLEAR CELL 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)              87
                                                             clus
vv                                                            9Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               383
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  91
  9Q GAIN WILD-TYPE  13 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   91
  9Q GAIN WILD-TYPE   13  389
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                13
  YES              91               389
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    77   2   0   2
  9Q GAIN WILD-TYPE 317  10   4  20
D18V13, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              77               317
  R1               2                10
  R2               0                 4
  RX               2                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       3                         5    62
  9Q GAIN WILD-TYPE     6                        26   278
D18V14, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               5                26
  WHITE                                  62               278
[1] 3 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  55
  9Q GAIN WILD-TYPE   6 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   55
  9Q GAIN WILD-TYPE    6  254
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              55               254
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    44  33
  10P GAIN WILD-TYPE 237 163
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                77                400 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                33                163 
$`10P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-3417 TCGA-21-1070 TCGA-21-1083 TCGA-21-5783 
        7.46        31.99        36.07       119.54        43.23        88.11 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1017 TCGA-22-5473 TCGA-33-4566 TCGA-33-6737 
       10.82         7.33        48.82        63.55       174.08        19.76 
TCGA-33-AASB TCGA-33-AASI TCGA-34-2609 TCGA-34-5928 TCGA-34-7107 TCGA-37-4133 
        6.94        44.19        31.27        18.15         1.12         7.82 
TCGA-37-4141 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-46-6025 TCGA-52-7811 
        0.39        27.02        18.38        27.91        10.65         8.75 
TCGA-56-7222 TCGA-56-8304 TCGA-56-A4BX TCGA-56-A5DR TCGA-58-A46L TCGA-60-2698 
        0.43         3.48        13.32         0.13        56.65        10.22 
TCGA-60-2712 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MG TCGA-66-2756 TCGA-66-2763 
        9.01        23.57        11.77        70.62         0.99         0.99 
TCGA-66-2778 TCGA-66-2782 TCGA-66-2792 TCGA-77-7140 TCGA-77-7142 TCGA-77-7463 
       19.00        12.00        30.02        20.78        42.28        46.78 
TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 
       26.40         9.63        54.41       132.36         5.92        42.41 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7843 TCGA-85-8350 TCGA-85-8352 TCGA-85-8582 
       11.97        12.99         1.15        22.45         5.29        13.94 
TCGA-85-A4JB TCGA-85-A50M TCGA-85-A510 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED 
       17.72        12.56        15.85        12.39         2.93        20.22 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-98-8022 TCGA-98-A53B TCGA-98-A53I 
       11.70        14.14        57.07        30.67         2.01        18.58 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ 
       51.78        45.37         2.89        37.22        24.00        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52W 
       22.78        83.57         3.65         0.43         8.58 

$`10P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
       12.20        75.75        79.46         4.80       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       23.54        92.15         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      154.32        49.94        27.19        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-21-A5DI TCGA-22-0940 
      119.80        31.63        41.69        33.93        32.19        21.99 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         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-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       31.73        64.93        14.63        44.25         0.79        54.28 
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-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
       56.32        16.64        22.06         7.63       133.74        98.01 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
       79.53       103.53       151.27        14.07        54.44         1.55 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ 
       27.02         4.70         0.30        36.62       110.99       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       27.16         2.63        61.61        31.50        28.96        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        67.79        56.38         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       16.93        30.94         4.96        27.19         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       20.91         3.95         0.43         0.39         6.58         8.12 
TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        7.46         6.81         3.39        47.80        74.07        44.75 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        70.03        60.79         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        27.39        36.39        15.58        35.64        35.70 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 
       17.88        17.06        40.21        22.49        38.66        33.11 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       12.36        24.89        21.47         5.46         3.81        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        7.76        66.51        13.38        11.77         2.93        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 
        9.73        14.20        12.03         9.99        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 
        0.39        29.95        28.34         5.46        30.35        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
       28.96         0.10        18.25         2.04         0.62         0.99 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.99         1.45         1.32         0.85         6.51         0.10 
TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
       17.49        26.89        17.00        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       15.81        20.94        19.23        17.85        21.04        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26         2.76         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-A46M 
       71.24        16.47        34.78        85.12        34.36        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       29.92        21.11         3.58        12.23        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       92.71        21.93        80.45        49.48        66.54        41.42 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       56.91        50.33        35.34        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MH 
       32.32        29.85        35.90        26.83       102.67        66.61 
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-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       89.29        78.28        16.37        25.41        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-66-2757 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-66-2767 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-66-2780 TCGA-66-2781 TCGA-66-2783 
       19.00         3.02         2.01        12.03         3.98        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-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
        5.03        10.06        54.08         4.01        49.05         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        6.64         6.94         8.02        13.35        16.18        14.73 
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        89.98 
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        15.75         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       86.76        53.95        37.81        82.92        12.59        53.92 
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-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 
       65.49        35.90         0.33       126.18       117.57        22.29 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6798 
       42.08        30.81        27.62        38.86         9.67         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        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
       16.87        34.52        10.09         0.76        13.22        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         0.72         7.76        14.63 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC 
       12.59         0.10        15.62        25.68        19.33        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 
       24.36        18.18        19.73        16.21        14.96         0.79 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
        3.65        24.92         9.50        11.77        14.07        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-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 
       21.04         0.16         4.01         5.03        26.63        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       17.69        49.87        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        8.42         2.76        30.81        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-J1-A4AH 
       18.15        27.02        21.21        20.32        20.71        19.10 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
       12.89        16.11        13.18        13.41        11.84         0.07 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM 
       64.08         4.54         1.22        13.74         4.21        39.85 
TCGA-NC-A5HO TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q 
       30.58        29.75        65.49        16.80        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89        11.18         0.20 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.13               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            174.08             154.32 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            17.720             19.475 
[1] "0.1 - 174.1 (17.7)" "0.0 - 154.3 (19.5)"
[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       75      134        1        50        78
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  10P GAIN MUTATED           0         13          4        2
  10P GAIN WILD-TYPE         3         49         17        5
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 12                 75
  STAGE IB                 17                134
  STAGE II                  1                  1
  STAGE IIA                13                 50
  STAGE IIB                14                 78
  STAGE III                 0                  3
  STAGE IIIA               13                 49
  STAGE IIIB                4                 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
  10P GAIN MUTATED    14  49  12   3
  10P GAIN WILD-TYPE  97 241  57  20
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               14                 97
  T2               49                241
  T3               12                 57
  T4                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                  N0  N1  N2  N3
  10P GAIN MUTATED    44  24   7   1
  10P GAIN WILD-TYPE 268 107  32   4
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               44                268
  N1               24                107
  N2                7                 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"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    63   2
  10P GAIN WILD-TYPE 341   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     63    2
  10P GAIN WILD-TYPE  341    5
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               63                341
  1                2                  5
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    13  65
  10P GAIN WILD-TYPE 114 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     13   65
  10P GAIN WILD-TYPE  114  301
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               13                114
  MALE                 65                301
[1] 2 2
[1] FALSE
D19V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                       2
  10P GAIN WILD-TYPE                                    13
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                         0
  10P GAIN WILD-TYPE                                       1
                    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                                                         394
D19V9, multiclass
                                                             clus
vv                                                            10P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG CLEAR CELL 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)               76
                                                             clus
vv                                                            10P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                394
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2  76
  10P GAIN WILD-TYPE  11 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   76
  10P GAIN WILD-TYPE   11  404
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                 11
  YES               76                404
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, continuous
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    62   0   1   2
  10P GAIN WILD-TYPE 332  12   3  20
D19V13, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               62                332
  R1                0                 12
  R2                1                  3
  RX                2                 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
  10P GAIN MUTATED       3                         8    51
  10P GAIN WILD-TYPE     6                        23   289
D19V14, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                8                 23
  WHITE                                   51                289
[1] 3 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  49
  10P GAIN WILD-TYPE   7 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   49
  10P GAIN WILD-TYPE    7  260
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               49                260
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    25  18
  10Q GAIN WILD-TYPE 256 178
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                43                434 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                18                178 
$`10Q GAIN MUTATED`
TCGA-18-3416 TCGA-21-1070 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-5473 
       31.99       119.54        43.23        33.93        10.82        63.55 
TCGA-33-4566 TCGA-33-4582 TCGA-33-AASI TCGA-34-2609 TCGA-34-5241 TCGA-34-5928 
      174.08       103.53        44.19        31.27        16.93        18.15 
TCGA-37-4141 TCGA-43-5670 TCGA-52-7811 TCGA-56-7222 TCGA-56-A5DR TCGA-60-2724 
        0.39        27.91         8.75         0.43         0.13        23.57 
TCGA-60-2726 TCGA-77-7140 TCGA-77-7142 TCGA-77-8130 TCGA-77-8150 TCGA-77-A5G7 
       11.77        20.78        42.28        82.92        54.41         5.92 
TCGA-85-6561 TCGA-85-7843 TCGA-85-8350 TCGA-85-8352 TCGA-85-A50M TCGA-85-A510 
       12.99         1.15        22.45         5.29        12.56        15.85 
TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED TCGA-94-7943 TCGA-94-A4VJ TCGA-98-A53B 
       12.39         2.93        20.22        11.70        14.14         2.01 
TCGA-98-A53I TCGA-NC-A5HG TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CX 
       18.58        51.78         2.89        24.00        14.73         3.65 
TCGA-NK-A7XE 
        0.43 

$`10Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       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         1.64        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
        6.18         2.79       154.32        49.94        27.19        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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       32.19        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
        1.74        14.10        27.02        48.82        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-22-5471 TCGA-22-5472 
       32.02        19.30         9.57        11.77        31.73        64.93 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       14.63        44.25         0.79        54.28        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-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 
       22.06         7.63       133.74        98.01        79.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
       14.07        54.44         1.55        19.76        27.02         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL 
        0.30        36.62         6.94       110.99       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 
        2.63        61.61        31.50        28.96        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
       67.79        56.38         9.07        23.24        12.00        30.94 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
        4.96         1.12        27.19         4.04        26.43        20.91 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        3.95         0.43         0.39         6.58         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        7.82         6.81         3.39        47.80        74.07        44.75 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        70.03        60.79         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        27.39        36.39        15.58        35.64        35.70 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
       17.88        17.06        40.21        22.49        38.66        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       33.11        18.38        12.36        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        3.81        19.59         7.76        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
        2.93        11.61         9.73        14.20        12.03         9.99 
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-56-1622 TCGA-56-5897 TCGA-56-5898 
        5.46        30.35        27.45        28.96         0.10        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
        2.04         0.62         0.99         0.99         1.45         1.32 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 
        0.85         6.51         0.10        17.49         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
       17.00        14.07         1.35        16.77         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.18        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS 
       19.23        13.32        17.85        21.04        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        2.76         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-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       41.42         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       42.64         3.19        32.32        29.85        35.90        26.83 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
      102.67        70.62        66.61        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-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       25.41        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-66-2773 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-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       49.05         2.73         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       16.18        14.73        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        89.98         0.49        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        15.75         6.51        86.76        53.95        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-77-8153 TCGA-77-8154 
       26.40        27.39         6.97         9.63        65.49        35.90 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 
        0.33       126.18       132.36       117.57        22.29        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       42.08        30.81        27.62        38.86         9.67        11.97 
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 
       14.07        16.87        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         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       19.33        17.72        14.96        24.36        18.18        19.73 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       16.21        14.96         0.79         3.65        24.92         9.50 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       11.77        14.07        22.62        10.59         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 
        4.01         5.26         2.30        21.04         0.16         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
        5.03        26.63        16.14        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       18.31        17.46        19.36        16.57         8.42         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
       30.81        30.67        21.34        27.16         3.88        18.15 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       27.02        21.21        20.32        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       16.11        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM 
        4.54         1.22        45.37        13.74         4.21        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       37.22        30.58        29.75        22.78        83.57        65.49 
TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
       16.80        33.07         3.72        12.72        43.89         8.58 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.13               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            174.08             154.32 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            16.930             19.315 
[1] "0.1 - 174.1 (16.9)" "0.0 - 154.3 (19.3)"
[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       79      142        2        54        84
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  10Q GAIN MUTATED           0          7          1        1
  10Q GAIN WILD-TYPE         3         55         20        6
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  8                 79
  STAGE IB                  9                142
  STAGE II                  0                  2
  STAGE IIA                 9                 54
  STAGE IIB                 8                 84
  STAGE III                 0                  3
  STAGE IIIA                7                 55
  STAGE IIIB                1                 20
  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  29   6   1
  10Q GAIN WILD-TYPE 103 261  63  22
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                8                103
  T2               29                261
  T3                6                 63
  T4                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                  N0  N1  N2  N3
  10Q GAIN MUTATED    24  14   4   0
  10Q GAIN WILD-TYPE 288 117  35   5
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               24                288
  N1               14                117
  N2                4                 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"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    36   1
  10Q GAIN WILD-TYPE 368   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     36    1
  10Q GAIN WILD-TYPE  368    6
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               36                368
  1                1                  6
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     8  36
  10Q GAIN WILD-TYPE 119 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      8   36
  10Q GAIN WILD-TYPE  119  330
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                8                119
  MALE                 36                330
[1] 2 2
[1] FALSE
D20V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED                                       1
  10Q GAIN WILD-TYPE                                    14
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED                                         0
  10Q GAIN WILD-TYPE                                       1
                    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                                                         427
D20V9, multiclass
                                                             clus
vv                                                            10Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG CLEAR CELL 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)               43
                                                             clus
vv                                                            10Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                427
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  42
  10Q GAIN WILD-TYPE  11 438
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   42
  10Q GAIN WILD-TYPE   11  438
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                 11
  YES               42                438
[1] 2 2
[1] FALSE
D20V11, continuous
D20V12, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    35   0   0   1
  10Q GAIN WILD-TYPE 359  12   4  21
D20V13, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               35                359
  R1                0                 12
  R2                0                  4
  RX                1                 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
  10Q GAIN MUTATED       2                         5    32
  10Q GAIN WILD-TYPE     7                        26   308
D20V14, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                5                 26
  WHITE                                   32                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"
D20V15, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  32
  10Q GAIN WILD-TYPE   7 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   32
  10Q GAIN WILD-TYPE    7  277
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               32                277
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    41  30
  11P GAIN WILD-TYPE 240 166
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                71                406 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                30                166 
$`11P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-21-1070 TCGA-21-1072 TCGA-21-1079 TCGA-21-5783 
        7.46         4.80       119.54        99.16        31.73        88.11 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-5491 TCGA-33-4582 
       14.10        20.48        48.33        24.13        56.32       103.53 
TCGA-33-4583 TCGA-34-5239 TCGA-34-8456 TCGA-39-5027 TCGA-39-5029 TCGA-39-5034 
      151.27        23.24        26.43        60.79        24.33        36.39 
TCGA-39-5036 TCGA-43-2578 TCGA-43-5668 TCGA-43-5670 TCGA-43-6771 TCGA-43-A474 
       35.64        22.49        18.38        27.91         5.46        11.61 
TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-6545 TCGA-56-7730 
       13.91         5.46        30.35        28.96         2.04         6.51 
TCGA-56-8308 TCGA-56-A49D TCGA-56-A4BX TCGA-60-2719 TCGA-60-2722 TCGA-63-A5MI 
       17.00        20.94        13.32        42.64        29.85        58.65 
TCGA-66-2734 TCGA-66-2744 TCGA-66-2765 TCGA-66-2766 TCGA-66-2770 TCGA-66-2777 
       43.10         0.99         2.01         1.02        23.01         2.01 
TCGA-66-2785 TCGA-66-2791 TCGA-68-7755 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 
        1.97         5.03         2.73        29.56        23.28        11.18 
TCGA-77-7142 TCGA-77-7463 TCGA-77-8007 TCGA-77-8139 TCGA-77-A5G1 TCGA-77-A5G3 
       42.28        46.78         6.51       104.09       132.36       117.57 
TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-6560 TCGA-85-7950 TCGA-85-8276 TCGA-90-7767 
        5.92        30.81        11.97        18.94        34.52         2.93 
TCGA-90-A4EE TCGA-92-8064 TCGA-94-7943 TCGA-96-8169 TCGA-96-A4JK TCGA-98-A53B 
       22.62         5.26        11.70        18.31        19.36         2.01 
TCGA-NC-A5HH TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NK-A7XE TCGA-O2-A52S 
        1.22         2.89        39.85         0.43        12.72 

$`11P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20        75.75        79.46       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
       92.15        31.99        36.07         1.64        86.96         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1075 
        2.79       154.32        49.94        27.19        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-21-A5DI 
       43.23        31.63        41.69        33.93        10.82        32.19 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       21.99         7.33        14.93         4.31        64.21         1.74 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       27.02        48.82        35.08         0.56        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       13.12        32.02        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       64.93        63.55        14.63        44.25         0.79        54.28 
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-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       16.64        22.06         7.63       133.74        98.01        79.53 
TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      174.08        14.07        54.44         1.55        19.76        27.02 
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-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       32.88        31.27        65.23        67.79        56.38         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       12.00        16.93        30.94        18.15         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       27.19         4.04        20.91         3.95         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        6.58         8.12         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        3.39        47.80        74.07        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 
       70.03         1.71         1.94        27.39        15.58        35.70 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       17.88        17.06        40.21        38.66        27.02        33.11 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
       12.36        24.89        21.47         3.81        19.59         7.76 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U 
       66.51        13.38        11.77         2.93         9.73        14.20 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       12.03         9.99        10.65         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 
       28.34         8.75        27.45         0.10        18.25         0.62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
        0.99         0.43         0.99         1.45         1.32         0.85 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        0.10        17.49         3.48        26.89        14.07         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       16.77         1.81        22.75         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.25        15.81        19.23        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         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-60-2696 TCGA-60-2697 
       56.65        35.24        29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
       49.48        66.54        41.42         9.01        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
       35.34        48.49         3.19        32.32        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ 
       26.83        11.77       102.67        70.62        66.61        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-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       16.37        25.41        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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        6.64         6.94         8.02        13.35        16.18        14.73 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 
       73.12        75.09        89.98        20.78         0.49        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
      106.95         0.16        15.75        86.76        53.95        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 
       82.92        12.59        53.92        39.09        17.72        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         9.63        54.41        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA 
       35.90         0.33       126.18        22.29        42.41        42.08 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86         9.67        12.99         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-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
       25.15        19.04        24.13        31.56        14.07        16.87 
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         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       13.94        12.59         0.10        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       17.72        14.96        24.36        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96         0.79        12.39         3.65 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q 
       24.92         9.50        11.77        14.07        20.22        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        2.70         3.48         4.01         2.30        21.04         0.16 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        4.01         5.03        26.63        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       49.87        57.07        17.46        16.57         8.42         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
       30.81        30.67        21.34        27.16         3.88        18.15 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       27.02        21.21        20.32        18.58        20.71        19.10 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
       12.89        16.11        13.18        13.41        11.84         0.07 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
       64.08         4.54        51.78        45.37        13.74         4.21 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT 
       37.22        30.58        24.00        14.73        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q 
       83.57        65.49         3.65        16.80        33.07         3.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89         8.58        11.18         0.20 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.43               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            151.27             174.08 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             20.94              19.00 
[1] "0.4 - 151.3 (20.9)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         0        9       24        0        13        12
  11P GAIN WILD-TYPE       2       78      127        2        50        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  11P GAIN MUTATED           1         11          3        0
  11P GAIN WILD-TYPE         2         51         18        7
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  9                 78
  STAGE IB                 24                127
  STAGE II                  0                  2
  STAGE IIA                13                 50
  STAGE IIB                12                 80
  STAGE III                 1                  2
  STAGE IIIA               11                 51
  STAGE IIIB                3                 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
  11P GAIN MUTATED    15  42  13   3
  11P GAIN WILD-TYPE  96 248  56  20
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               15                 96
  T2               42                248
  T3               13                 56
  T4                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                  N0  N1  N2  N3
  11P GAIN MUTATED    46  15   9   1
  11P GAIN WILD-TYPE 266 116  30   4
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               46                266
  N1               15                116
  N2                9                 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    63   0
  11P GAIN WILD-TYPE 341   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     63    0
  11P GAIN WILD-TYPE  341    7
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               63                341
  1                0                  7
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    14  59
  11P GAIN WILD-TYPE 113 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     14   59
  11P GAIN WILD-TYPE  113  307
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               14                113
  MALE                 59                307
[1] 2 2
[1] FALSE
D21V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED                                       2
  11P GAIN WILD-TYPE                                    13
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED                                         0
  11P GAIN WILD-TYPE                                       1
                    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                                                            70
  11P GAIN WILD-TYPE                                                         400
D21V9, multiclass
                                                             clus
vv                                                            11P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG CLEAR CELL 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)               70
                                                             clus
vv                                                            11P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                400
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  71
  11P GAIN WILD-TYPE  11 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   71
  11P GAIN WILD-TYPE   11  409
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 2                 11
  YES               71                409
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, continuous
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    56   3   1   4
  11P GAIN WILD-TYPE 338   9   3  18
D21V13, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               56                338
  R1                3                  9
  R2                1                  3
  RX                4                 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
  11P GAIN MUTATED       2                         2    50
  11P GAIN WILD-TYPE     7                        29   290
D21V14, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                2                 29
  WHITE                                   50                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"
D21V15, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  39
  11P GAIN WILD-TYPE   7 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   39
  11P GAIN WILD-TYPE    7  270
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               39                270
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    54  34
  11Q GAIN WILD-TYPE 227 162
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                88                389 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                34                162 
$`11Q GAIN MUTATED`
TCGA-18-3410 TCGA-21-1070 TCGA-21-1072 TCGA-21-1079 TCGA-21-5786 TCGA-22-1012 
        4.80       119.54        99.16        31.73        33.93        14.10 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-5491 TCGA-33-4582 TCGA-33-4583 
       20.48        48.33        24.13        56.32       103.53       151.27 
TCGA-33-AASD TCGA-34-5231 TCGA-34-5239 TCGA-34-8455 TCGA-34-8456 TCGA-37-4132 
      110.99        65.23        23.24         4.04        26.43         7.46 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5029 TCGA-39-5034 
        6.81         0.39         3.39        47.80        24.33        36.39 
TCGA-39-5036 TCGA-43-2578 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 
       35.64        22.49        18.38        27.91        12.36         5.46 
TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7730 TCGA-56-8308 
       30.35        28.96        18.25         2.04         6.51        17.00 
TCGA-56-A49D TCGA-56-A5DR TCGA-60-2719 TCGA-60-2720 TCGA-63-A5MI TCGA-63-A5MV 
       20.94         0.13        42.64         3.19        58.65        36.16 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2759 TCGA-66-2763 TCGA-66-2777 
       43.10         2.01        21.07        25.05         0.99         2.01 
TCGA-66-2781 TCGA-66-2786 TCGA-66-2789 TCGA-66-2791 TCGA-68-7755 TCGA-77-6842 
        3.98        25.97         4.04         5.03         2.73        29.56 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 
       23.28        11.18         0.49        42.28       106.95        46.78 
TCGA-77-8007 TCGA-77-8139 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GB 
        6.51       104.09        35.90       132.36         5.92        30.81 
TCGA-85-6560 TCGA-85-7843 TCGA-85-7950 TCGA-85-8276 TCGA-85-8353 TCGA-85-A4CN 
       11.97         1.15        18.94        34.52         3.09        19.33 
TCGA-85-A4JB TCGA-85-A510 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4EE TCGA-92-8064 
       17.72        15.85        12.39         2.93        22.62         5.26 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-A4JK TCGA-98-A53B TCGA-LA-A7SW TCGA-NC-A5HH 
       11.70        14.14        19.36         2.01        13.41         1.22 
TCGA-NC-A5HM TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-O2-A52S 
       39.85        14.73        29.75        12.72 

$`11Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       23.54        92.15        31.99        36.07         1.64        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
        6.18         2.79       154.32        49.94        27.19        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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       32.19        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 
        1.74        27.02        48.82        35.08         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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       31.73        64.93        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 
       54.28        71.34        79.20        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
       62.86        16.64        22.06         7.63       133.74        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
       79.53       174.08        14.07        54.44         1.55        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI 
       27.02         4.70         0.30        36.62         6.94        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 
       32.88        31.27        67.79        56.38         9.07        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        30.94        18.15         4.96         1.12        27.19 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       20.91         3.95         0.43         0.39         6.58         8.12 
TCGA-37-4133 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        7.82        74.07        44.75        68.58        55.20        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 
       60.79         1.71         1.94        27.39        15.58        35.70 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       17.88        17.06        40.21        38.66        27.02        33.11 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
       24.89        21.47         3.81        19.59         7.76        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
       13.38        11.77         2.93        11.61         9.73        14.20 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       12.03         9.99        10.65        13.91         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 
       29.95        28.34         5.46         8.75        27.45         0.10 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
        0.62         0.99         0.43         0.99         1.45         1.32 
TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        0.85         0.10        17.49         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
        9.93        20.25        15.81        19.23        13.32        17.85 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       21.04        18.74         0.26         2.76         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-60-2696 
       34.36        56.65        35.24        29.92        21.11         3.58 
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-60-2711 TCGA-60-2712 TCGA-60-2713 
       80.45        49.48        66.54        41.42         9.01        56.91 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
       50.33        35.34        48.49        32.32        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH 
       23.57        26.83        11.77       102.67        70.62        66.61 
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-A5MU TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        25.41        53.88        34.59        16.96 
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-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       21.01         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
       23.01        19.00         3.02        19.00        12.03        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2792 
       24.95         1.97        40.01        22.98        22.98        30.02 
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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 
        8.02        13.35        16.18        14.73        73.12        75.09 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7335 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 
       89.98        20.78        70.13         0.16        15.75        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       53.95        37.81        82.92        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         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 
       54.41        65.49         0.33       126.18       117.57        22.29 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 
       42.41        42.08        27.62        38.86         9.67        12.99 
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-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       29.95        25.15        19.04        24.13        31.56        14.07 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       16.87        10.09         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         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC 
       13.94        12.59         0.10        15.62        25.68        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
       24.36        18.18        19.73        12.56        16.21        14.96 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 
        0.79         3.65        24.92         9.50        11.77        14.07 
TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
       20.22        10.59         2.70         3.48         4.01         2.30 
TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 
       21.04         0.16         4.01         5.03        26.63        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       17.69        49.87        57.07        18.31        17.46        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
        8.42         2.76        30.81        30.67        21.34        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
        3.88        18.15        27.02        21.21        20.32        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
       20.71        19.10        12.89        16.11        13.18        11.84 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ 
        0.07        64.08         4.54        51.78        45.37        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT 
        4.21         2.89        37.22        30.58        24.00        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N 
       83.57        65.49         3.65        16.80         0.43        33.07 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        43.89         8.58        11.18         0.20 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.13               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            151.27             174.08 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            19.345             19.040 
[1] "0.1 - 151.3 (19.3)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         0       17       23        0        14        13
  11Q GAIN WILD-TYPE       2       70      128        2        49        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  11Q GAIN MUTATED           1         15          4        3
  11Q GAIN WILD-TYPE         2         47         17        4
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 17                 70
  STAGE IB                 23                128
  STAGE II                  0                  2
  STAGE IIA                14                 49
  STAGE IIB                13                 79
  STAGE III                 1                  2
  STAGE IIIA               15                 47
  STAGE IIIB                4                 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  46  17   3
  11Q GAIN WILD-TYPE  87 244  52  20
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               24                 87
  T2               46                244
  T3               17                 52
  T4                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                  N0  N1  N2  N3
  11Q GAIN MUTATED    56  20  10   2
  11Q GAIN WILD-TYPE 256 111  29   3
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               56                256
  N1               20                111
  N2               10                 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"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    75   3
  11Q GAIN WILD-TYPE 329   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     75    3
  11Q GAIN WILD-TYPE  329    4
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               75                329
  1                3                  4
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    23  67
  11Q GAIN WILD-TYPE 104 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     23   67
  11Q GAIN WILD-TYPE  104  299
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               23                104
  MALE                 67                299
[1] 2 2
[1] FALSE
D22V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED                                       3
  11Q GAIN WILD-TYPE                                    12
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED                                         1
  11Q GAIN WILD-TYPE                                       0
                    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                                                            85
  11Q GAIN WILD-TYPE                                                         385
D22V9, multiclass
                                                             clus
vv                                                            11Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               85
                                                             clus
vv                                                            11Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                385
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  89
  11Q GAIN WILD-TYPE  12 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   89
  11Q GAIN WILD-TYPE   12  391
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 1                 12
  YES               89                391
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    73   3   0   5
  11Q GAIN WILD-TYPE 321   9   4  17
D22V13, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               73                321
  R1                3                  9
  R2                0                  4
  RX                5                 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    63
  11Q GAIN WILD-TYPE     7                        28   277
D22V14, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                   63                277
[1] 3 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  50
  11Q GAIN WILD-TYPE   7 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   50
  11Q GAIN WILD-TYPE    7  259
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               50                259
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   126  91
  12P GAIN WILD-TYPE 155 105
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               217                260 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                91                105 
$`12P GAIN MUTATED`
TCGA-18-3410 TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 
        4.80        11.34        36.07        86.96         6.18       154.32 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1079 TCGA-21-1083 
      119.54        46.88        99.16        34.78        31.73        43.23 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1012 TCGA-22-1017 
       31.63        33.93        10.82        32.19        14.10        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
       20.48        35.08        48.33        24.13        38.17        34.75 
TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 TCGA-22-5482 
       13.12        31.73        63.55        44.25        71.34        11.74 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 
       62.86        56.32         7.63        98.01       174.08       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASJ 
      151.27        14.07        19.76        27.02       110.99       118.36 
TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 
        2.63        28.96        31.27        65.23        23.24        12.00 
TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-37-3792 
       16.93        18.15         1.12         4.04        26.43         0.39 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
       44.75        68.58        36.39        15.58        35.64        35.70 
TCGA-39-5040 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 TCGA-43-6771 
       17.06        27.02        33.11        27.91        21.47         5.46 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 
       13.38        11.77        11.61         9.73        12.03         9.99 
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-52-7812 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 
        8.75        27.45         2.04         0.62         0.43         0.99 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8504 
        0.85         6.51        17.49         3.48        17.00        16.77 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DR TCGA-58-8387 TCGA-58-A46K 
       15.81        19.23        13.32         0.13        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-60-2711 TCGA-60-2712 TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       41.42         9.01        42.64        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
       11.77       102.67        66.61        58.65        59.97        45.57 
TCGA-63-A5MR TCGA-63-A5MW TCGA-66-2727 TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 
       89.29        53.88        16.96         0.99         2.01         0.99 
TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2777 TCGA-66-2781 
       21.01         1.02         2.01         7.07         2.01         3.98 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 
        1.97        40.01        10.06        54.08        49.05         2.73 
TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
        6.64         8.02        13.35        16.18        14.73        29.56 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 
       20.78         0.49        42.28       106.95        46.78        15.75 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8143 
       53.95        37.81        82.92        53.92        17.72        26.40 
TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        9.63         0.33       132.36       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
       42.41        27.62        11.97        36.53        34.95        32.91 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 
       18.94        25.15        19.04        24.13        31.56        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 TCGA-85-8481 
       10.09         0.76        22.45         5.29        32.71         7.76 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A510 
        0.10        15.62        19.33        14.96        19.73        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
       14.96         0.79        12.39         2.93        11.77        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7557 TCGA-94-7943 
       10.59         2.70         3.48         5.26         0.16        11.70 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-A538 TCGA-98-A53B 
       14.14        16.14        17.69        19.36        27.16         2.01 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
       18.58        20.71        19.10        16.11        13.18        11.84 
TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
        0.07         4.54        51.78         1.22        13.74         4.21 
TCGA-NC-A5HM TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       39.85        14.73        29.75         0.43        33.07         3.72 
TCGA-O2-A52W 
        8.58 

$`12P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 
       12.20         7.46        75.75        79.46       117.57        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 
       92.15        31.99         1.64         2.79        49.94        27.19 
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-22-1000 TCGA-22-1002 
       88.11        41.69        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4596 TCGA-22-4605 TCGA-22-4607 
       64.21         1.74        27.02         0.56        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 
        9.57        11.77        64.93        14.63         0.79        54.28 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 
       79.20        18.84        30.12        16.64        22.06       133.74 
TCGA-33-4547 TCGA-33-4587 TCGA-33-4589 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       79.53        54.44         1.55         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 
        6.94        44.19        27.16        61.61        31.50        32.88 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       67.79        56.38         9.07        30.94         4.96        27.19 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       20.91         3.95         0.43         6.58         8.12         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        47.80        74.07 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        70.03        60.79         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 
       27.39        17.88        40.21        22.49        38.66        18.38 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
       12.36        24.89         3.81        19.59         7.76        66.51 
TCGA-43-8118 TCGA-43-A56U TCGA-51-4080 TCGA-52-7622 TCGA-56-1622 TCGA-56-5897 
        2.93        14.20         0.39        28.34        28.96         0.10 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-8307 
       18.25         0.99         1.45         1.32         0.10        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         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
        9.93        20.25        20.94        17.85        21.04        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.26         2.76         0.03        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-60-2696 TCGA-60-2697 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
        3.58        12.23        21.93        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
       50.33        35.34        48.49         3.19        32.32        29.85 
TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT 
       70.62        14.99        11.34        25.28        78.28        16.37 
TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       25.41        36.16        34.59        43.10         2.01        21.07 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        1.02         0.92        43.99        25.05         0.99         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
        2.01        23.01        19.00         3.02        19.00        12.03 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       12.00        24.95        25.97        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7757 TCGA-77-6843 TCGA-77-6844 
        5.03        30.02         4.01         6.94        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 TCGA-77-8007 
       23.28        11.18        89.98        70.13         0.16         6.51 
TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
       86.76        12.59        39.09       104.09        11.54        27.39 
TCGA-77-8145 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5GA 
        6.97        54.41        65.49        35.90       126.18        42.08 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 
       30.81        38.86         9.67        12.99         6.41        31.30 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 
        1.38         1.15        29.95        14.07        16.87        13.22 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 
       16.77         3.09         2.01         0.72        14.63        13.94 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       12.59        25.68        17.72        24.36        18.18        12.56 
TCGA-85-A50Z TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED 
       16.21         3.65        24.92         9.50        14.07        20.22 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         2.30        21.04         4.01         5.03        26.63 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       49.87        57.07        18.31        17.46        16.57         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A 
        2.76        30.81        30.67        21.34         3.88        18.15 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HE 
       27.02        21.21        20.32        12.89        13.41        64.08 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT 
       45.37         2.89        37.22        30.58        24.00        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52S TCGA-O2-A52V 
       83.57        65.49         3.65        16.80        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 
            174.08             133.74 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            19.040             19.445 
[1] "0.1 - 174.1 (19.0)" "0.0 - 133.7 (19.4)"
[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        33        44
  12P GAIN WILD-TYPE       0       55       86        1        30        48
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  12P GAIN MUTATED           1         34         10        2
  12P GAIN WILD-TYPE         2         28         11        5
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 32                 55
  STAGE IB                 65                 86
  STAGE II                  1                  1
  STAGE IIA                33                 30
  STAGE IIB                44                 48
  STAGE III                 1                  2
  STAGE IIIA               34                 28
  STAGE IIIB               10                 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
  12P GAIN MUTATED    40 138  33  14
  12P GAIN WILD-TYPE  71 152  36   9
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               40                 71
  T2              138                152
  T3               33                 36
  T4               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                  N0  N1  N2  N3
  12P GAIN MUTATED   137  63  22   1
  12P GAIN WILD-TYPE 175  68  17   4
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0              137                175
  N1               63                 68
  N2               22                 17
  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   186   2
  12P GAIN WILD-TYPE 218   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    186    2
  12P GAIN WILD-TYPE  218    5
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0              186                218
  1                2                  5
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    43 182
  12P GAIN WILD-TYPE  84 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     43  182
  12P GAIN WILD-TYPE   84  184
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               43                 84
  MALE                182                184
[1] 2 2
[1] FALSE
D23V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                       7
  12P GAIN WILD-TYPE                                     8
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                         0
  12P GAIN WILD-TYPE                                       1
                    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                                                           216
  12P GAIN WILD-TYPE                                                         254
D23V9, multiclass
                                                             clus
vv                                                            12P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              216
                                                             clus
vv                                                            12P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                254
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     7 218
  12P GAIN WILD-TYPE   6 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7  218
  12P GAIN WILD-TYPE    6  262
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 7                  6
  YES              218                262
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, continuous
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED   177   6   2  11
  12P GAIN WILD-TYPE 217   6   2  11
D23V13, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0              177                217
  R1                6                  6
  R2                2                  2
  RX               11                 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   162
  12P GAIN WILD-TYPE     5                        15   178
D23V14, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN               16                 15
  WHITE                                  162                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"
D23V15, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     4 144
  12P GAIN WILD-TYPE   4 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4  144
  12P GAIN WILD-TYPE    4  165
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              144                165
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    83  63
  12Q GAIN WILD-TYPE 198 133
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               146                331 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                63                133 
$`12Q GAIN MUTATED`
TCGA-18-3410 TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 
        4.80        11.34        36.07        86.96         6.18       154.32 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1083 TCGA-21-5786 
      119.54        46.88        99.16        34.78        43.23        33.93 
TCGA-21-5787 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
       10.82        27.02        48.82        20.48        35.08        48.33 
TCGA-22-4601 TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 TCGA-22-5480 TCGA-22-5482 
       34.75        13.12        31.73        63.55        71.34        11.74 
TCGA-22-5491 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       56.32         7.63        98.01       103.53       151.27        14.07 
TCGA-33-6737 TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 
       19.76         2.63        28.96        31.27        65.23        23.24 
TCGA-34-7107 TCGA-34-8455 TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 TCGA-39-5011 
        1.12         4.04         0.39         8.12         3.39        47.80 
TCGA-39-5019 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 
       44.75        15.58        35.64        35.70        27.02        33.11 
TCGA-43-6771 TCGA-43-8116 TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 
        5.46        11.77         9.73         9.99        10.65         0.39 
TCGA-52-7809 TCGA-52-7812 TCGA-56-6546 TCGA-56-7582 TCGA-56-7822 TCGA-56-8304 
        5.46        27.45         0.62         0.85        17.49         3.48 
TCGA-56-8308 TCGA-56-A4BX TCGA-56-A5DR TCGA-58-A46K TCGA-60-2695 TCGA-60-2698 
       17.00        13.32         0.13        34.36        21.11        10.22 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2712 TCGA-60-2715 TCGA-60-2719 
       37.94        92.71        80.45         9.01        35.34        42.64 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ 
       23.57        26.83        11.77       102.67        66.61        59.97 
TCGA-63-A5ML TCGA-63-A5MR TCGA-66-2754 TCGA-66-2756 TCGA-66-2766 TCGA-66-2767 
       45.57        89.29         2.01         0.99         1.02         2.01 
TCGA-66-2781 TCGA-66-2787 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 
        3.98        40.01        10.06        54.08        49.05         2.73 
TCGA-68-7756 TCGA-68-8251 TCGA-77-6842 TCGA-77-7140 TCGA-77-7142 TCGA-77-7465 
        6.64        13.35        29.56        20.78        42.28        15.75 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8143 TCGA-77-8148 
       53.95        37.81        82.92        53.92        26.40         9.63 
TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-7950 
       54.41        35.90       117.57         5.92        27.62        18.94 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8353 
       24.13        31.56        34.52        10.09        22.45         3.09 
TCGA-85-8354 TCGA-85-8664 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A510 
       32.71         0.10        19.33        14.96        19.73        15.85 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
        0.79         3.65         2.93        11.77        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-94-7557 TCGA-94-7943 TCGA-98-8023 TCGA-98-A53B 
        2.70         3.48         0.16        11.70        21.34         2.01 
TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HD TCGA-NC-A5HF 
       18.58        19.10        16.11        13.18         0.07         4.54 
TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HQ TCGA-NC-A5HR 
       51.78        13.74         4.21        39.85        14.73        29.75 
TCGA-NK-A7XE TCGA-O2-A52Q 
        0.43         3.72 

$`12Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 
       12.20         7.46        75.75        79.46       117.57        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 
       92.15        31.99         1.64         2.79        49.94        27.19 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       70.16        60.89        15.58        31.73       122.43         9.34 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 
      119.80        31.63        88.11        41.69        32.19        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
        7.33        14.93         4.31        64.21         1.74        14.10 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       24.13         0.56        38.17        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       11.77        64.93        14.63        44.25         0.79        54.28 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 
       79.20        18.84        30.12        62.86        16.64        22.06 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 
      133.74        79.53       174.08        54.44         1.55        27.02 
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-34-2604 TCGA-34-2608 TCGA-34-5232 
      118.36        27.16        61.61        31.50        32.88        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       56.38         9.07        12.00        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        4.96        27.19        26.43        20.91         3.95         0.43 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 
        6.58         7.46         7.82         6.81         0.39        74.07 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        70.03        60.79         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
        1.94        27.39        36.39        17.88        17.06        40.21 
TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       22.49        38.66        18.38        27.91        12.36        24.89 
TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       21.47         3.81        19.59         7.76        66.51        13.38 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4080 
        2.93        11.61        14.20        12.03        13.91         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 
       29.95        28.34        30.35         8.75        28.96         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       18.25         2.04         0.99         0.43         0.99         1.45 
TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        1.32         6.51         0.10        26.89        14.07         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       16.77         1.81        22.75         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
       20.25        15.81        20.94        19.23        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.26         2.76         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-58-A46N TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2707 
       35.24        29.92         3.58        12.23        96.82        21.93 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       49.48        66.54        41.42        56.91        50.33        48.49 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MG TCGA-63-A5MI 
        3.19        32.32        29.85        35.90        70.62        58.65 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       14.99        11.34        25.28        78.28        16.37        25.41 
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-66-2755 TCGA-66-2757 TCGA-66-2758 
       21.07         0.99         1.02         0.92        43.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
       25.05         0.99         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-66-2786 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-66-2795 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I 
        5.03        30.02         4.01         6.94         8.02        16.18 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       14.73        73.12        75.09        23.28        11.18        89.98 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
        0.49        70.13       106.95         0.16        46.78         6.51 
TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       86.76        12.59        39.09        17.72       104.09        11.54 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       27.39         6.97        65.49         0.33       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 
       22.29        42.41        42.08        30.81        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       11.97        12.99         6.41        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 
       32.91         1.38         1.15        29.95        25.15        19.04 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
       14.07        16.87         0.76        13.22        16.77         5.29 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01         0.72         7.76        14.63        13.94        12.59 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       15.62        25.68        17.72        24.36        18.18        12.56 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
       16.21        14.96        12.39        24.92         9.50        14.07 
TCGA-90-A4ED TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 
       20.22         4.01         5.26         2.30        21.04         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 
        5.03        26.63        14.14        16.14        17.69        49.87 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
       57.07        18.31        17.46        19.36        16.57         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
        2.76        30.81        30.67        27.16         3.88        18.15 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A7SW 
       27.02        21.21        20.32        20.71        12.89        13.41 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN 
       11.84        64.08         1.22        45.37         2.89        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       30.58        24.00        22.78        83.57        65.49         3.65 
TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       16.80        33.07        12.72        43.89         8.58        11.18 
TCGA-XC-AA0X 
        0.20 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            154.32             174.08 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            19.745             19.000 
[1] "0.1 - 154.3 (19.7)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0       24       38        1        21        29
  12Q GAIN WILD-TYPE       2       63      113        1        42        63
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  12Q GAIN MUTATED           1         25          9        2
  12Q GAIN WILD-TYPE         2         37         12        5
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 24                 63
  STAGE IB                 38                113
  STAGE II                  1                  1
  STAGE IIA                21                 42
  STAGE IIB                29                 63
  STAGE III                 1                  2
  STAGE IIIA               25                 37
  STAGE IIIB                9                 12
  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  85  22  12
  12Q GAIN WILD-TYPE  80 205  47  11
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               31                 80
  T2               85                205
  T3               22                 47
  T4               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                  N0  N1  N2  N3
  12Q GAIN MUTATED    83  47  17   1
  12Q GAIN WILD-TYPE 229  84  22   4
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               83                229
  N1               47                 84
  N2               17                 22
  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   129   2
  12Q GAIN WILD-TYPE 275   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    129    2
  12Q GAIN WILD-TYPE  275    5
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0              129                275
  1                2                  5
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    26 124
  12Q GAIN WILD-TYPE 101 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     26  124
  12Q GAIN WILD-TYPE  101  242
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               26                101
  MALE                124                242
[1] 2 2
[1] FALSE
D24V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                       5
  12Q GAIN WILD-TYPE                                    10
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                         0
  12Q GAIN WILD-TYPE                                       1
                    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                                                           144
  12Q GAIN WILD-TYPE                                                         326
D24V9, multiclass
                                                             clus
vv                                                            12Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG CLEAR CELL 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)              144
                                                             clus
vv                                                            12Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                326
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4 146
  12Q GAIN WILD-TYPE   9 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4  146
  12Q GAIN WILD-TYPE    9  334
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 4                  9
  YES              146                334
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED   124   4   1   6
  12Q GAIN WILD-TYPE 270   8   3  16
D24V13, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0              124                270
  R1                4                  8
  R2                1                  3
  RX                6                 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
  12Q GAIN MUTATED       2                         8   109
  12Q GAIN WILD-TYPE     7                        23   231
D24V14, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                8                 23
  WHITE                                  109                231
[1] 3 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  93
  12Q GAIN WILD-TYPE   5 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   93
  12Q GAIN WILD-TYPE    5  216
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               93                216
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    21  13
  13Q GAIN WILD-TYPE 260 183
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                34                443 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                183 
$`13Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3412 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-22-4599 
        7.46        11.34        31.73         9.34       119.80        38.17 
TCGA-33-4533 TCGA-33-AASB TCGA-34-8455 TCGA-34-A5IX TCGA-37-4130 TCGA-39-5034 
      133.74         6.94         4.04        20.91         8.12        36.39 
TCGA-39-5035 TCGA-43-2576 TCGA-43-7657 TCGA-43-A56V TCGA-51-4081 TCGA-52-7810 
       15.58        40.21         7.76        12.03        29.95        30.35 
TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 TCGA-56-7822 TCGA-56-A4BX TCGA-60-2698 
        0.10        18.25         0.99        17.49        13.32        10.22 
TCGA-63-A5MT TCGA-66-2737 TCGA-66-2791 TCGA-85-7696 TCGA-85-7843 TCGA-85-A4JC 
       16.37         2.01         5.03        36.53         1.15        14.96 
TCGA-85-A50M TCGA-90-A59Q TCGA-94-7943 TCGA-MF-A522 
       12.56        10.59        11.70        11.84 

$`13Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
       12.20        75.75        79.46         4.80       117.57        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
       92.15        31.99        36.07         1.64        86.96         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
        2.79       154.32        49.94        27.19       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 
       99.16        70.16        60.89        34.78        15.58       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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       32.19        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
        1.74        14.10        27.02        48.82        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       48.33        24.13         0.56        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        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        54.28        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-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       22.06         7.63        98.01        79.53       174.08       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      151.27        14.07        54.44         1.55        19.76        27.02 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        4.70         0.30        36.62       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       27.16         2.63        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.27        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       12.00        16.93        30.94        18.15         4.96         1.12 
TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       27.19        26.43         3.95         0.43         0.39         6.58 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        7.46         7.82         6.81         0.39         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       74.07        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 
        1.71        24.33         1.94        27.39        35.64        35.70 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       17.88        17.06        22.49        38.66        27.02        33.11 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       18.38        27.91        12.36        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        3.81        19.59        66.51        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       11.61         9.73        14.20         9.99        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
        0.39         0.39        28.34         5.46         8.75        27.45 
TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
       28.96         2.04         0.62         0.99         0.43         1.45 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        1.32         0.85         6.51         0.10         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
       17.00        14.07         1.35        16.77         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.18        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
       19.23        17.85        21.04        18.74         0.13         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        2.76         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-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       29.92        21.11         3.58        12.23        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       92.71        21.93        80.45        49.48        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
        9.01        56.91        50.33        35.34        48.49        42.64 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        3.19        32.32        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ 
       11.77       102.67        70.62        66.61        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-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       25.41        36.16        53.88        34.59        16.96        43.10 
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-66-2757 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-66-2792 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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        6.64         6.94         8.02        13.35        16.18        14.73 
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        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       20.78         0.49        42.28        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        15.75         6.51        86.76        53.95        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       82.92        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       11.54        26.40        27.39         6.97         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       65.49        35.90         0.33       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 
       38.86         9.67        11.97        12.99         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        14.07        16.87        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         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       13.94        12.59         0.10        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
       17.72        24.36        18.18        19.73        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       14.96         0.79        12.39         3.65        24.92         9.50 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 
        2.93        11.77        14.07        20.22        22.62         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        3.48         4.01         5.26         2.30        21.04         0.16 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        4.01         5.03        26.63        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       49.87        57.07        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
        8.42         2.76        30.81        30.67        21.34        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       18.58        20.71        19.10        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       13.41         0.07        64.08         4.54        51.78         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN 
       45.37        13.74         4.21         2.89        39.85        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       30.58        24.00        14.73        29.75        22.78        83.57 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       65.49         3.65        16.80         0.43        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89         8.58        11.18         0.20 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.10               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            133.74             174.08 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            12.295             19.760 
[1] "0.1 - 133.7 (12.3)" "0.0 - 174.1 (19.8)"
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         0        6        8        0         6         9
  13Q GAIN WILD-TYPE       2       81      143        2        57        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  13Q GAIN MUTATED           0          4          1        1
  13Q GAIN WILD-TYPE         3         58         20        6
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  6                 81
  STAGE IB                  8                143
  STAGE II                  0                  2
  STAGE IIA                 6                 57
  STAGE IIB                 9                 83
  STAGE III                 0                  3
  STAGE IIIA                4                 58
  STAGE IIIB                1                 20
  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  20   7   1
  13Q GAIN WILD-TYPE 104 270  62  22
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                7                104
  T2               20                270
  T3                7                 62
  T4                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                  N0  N1  N2  N3
  13Q GAIN MUTATED    23   8   2   1
  13Q GAIN WILD-TYPE 289 123  37   4
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               23                289
  N1                8                123
  N2                2                 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    26   1
  13Q GAIN WILD-TYPE 378   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     26    1
  13Q GAIN WILD-TYPE  378    6
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               26                378
  1                1                  6
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     8  27
  13Q GAIN WILD-TYPE 119 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      8   27
  13Q GAIN WILD-TYPE  119  339
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                8                119
  MALE                 27                339
[1] 2 2
[1] FALSE
D25V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED                                       0
  13Q GAIN WILD-TYPE                                    15
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED                                         0
  13Q GAIN WILD-TYPE                                       1
                    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                                                            34
  13Q GAIN WILD-TYPE                                                         436
D25V9, multiclass
                                                             clus
vv                                                            13Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      0
  LUNG CLEAR CELL 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)               34
                                                             clus
vv                                                            13Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       15
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                436
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1  34
  13Q GAIN WILD-TYPE  12 446
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   34
  13Q GAIN WILD-TYPE   12  446
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 1                 12
  YES               34                446
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    26   1   0   2
  13Q GAIN WILD-TYPE 368  11   4  20
D25V13, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               26                368
  R1                1                 11
  R2                0                  4
  RX                2                 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
  13Q GAIN MUTATED       3                         4    25
  13Q GAIN WILD-TYPE     6                        27   315
D25V14, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                4                 27
  WHITE                                   25                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"
D25V15, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  29
  13Q GAIN WILD-TYPE   8 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   29
  13Q GAIN WILD-TYPE    8  280
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               29                280
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    78  44
  14Q GAIN WILD-TYPE 203 152
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               122                355 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                44                152 
$`14Q GAIN MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3421 TCGA-18-5592 
       75.75       117.57        11.34        92.15        86.96        49.94 
TCGA-21-1076 TCGA-21-1079 TCGA-21-1082 TCGA-21-5786 TCGA-22-4591 TCGA-22-4593 
       60.89        31.73       119.80        33.93        20.48        35.08 
TCGA-22-4595 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 
       24.13        31.73        22.06         7.63       133.74       174.08 
TCGA-33-4582 TCGA-33-4589 TCGA-33-6737 TCGA-33-AASD TCGA-33-AASI TCGA-34-8455 
      103.53         1.55        19.76       110.99        44.19         4.04 
TCGA-34-8456 TCGA-37-3792 TCGA-37-5819 TCGA-39-5011 TCGA-39-5029 TCGA-39-5031 
       26.43         0.39         3.39        47.80        24.33        27.39 
TCGA-39-5037 TCGA-43-2578 TCGA-43-6143 TCGA-43-6771 TCGA-43-8118 TCGA-43-A474 
       35.70        22.49        12.36         5.46         2.93        11.61 
TCGA-43-A56V TCGA-46-6025 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-56-1622 
       12.03        10.65        29.95        28.34         8.75        28.96 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-7730 TCGA-56-8304 
       18.25         2.04         0.62         1.32         6.51         3.48 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T 
       16.77         1.18        15.81        20.94        18.74         2.76 
TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 
       34.78        35.24        29.92        10.22        92.71        21.93 
TCGA-60-2708 TCGA-60-2719 TCGA-60-2722 TCGA-60-2724 TCGA-63-A5MG TCGA-63-A5MI 
       80.45        42.64        29.85        23.57        70.62        58.65 
TCGA-63-A5MU TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2771 
       25.41         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-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 
       23.28        11.18        42.28       106.95        46.78         6.51 
TCGA-77-8130 TCGA-77-8136 TCGA-77-8139 TCGA-77-8143 TCGA-77-8150 TCGA-77-8153 
       82.92        39.09       104.09        26.40        54.41        65.49 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6175 TCGA-85-6561 TCGA-85-7698 
      117.57        22.29        42.41         9.67        12.99        31.30 
TCGA-85-8353 TCGA-85-8355 TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A5B5 
        3.09         2.01        17.72        18.18        12.56         3.65 
TCGA-92-7340 TCGA-92-7341 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A538 TCGA-98-A539 
        2.70         3.48        19.36         2.76        27.16         3.88 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HM TCGA-NC-A5HP 
       12.89        16.11        51.78        45.37        39.85        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q 
       14.73        29.75        83.57         3.65        33.07         3.72 
TCGA-O2-A52V TCGA-O2-A52W 
       43.89         8.58 

$`14Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
       12.20         7.46        79.46         4.80        23.54        31.99 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
       36.07         1.64         6.18         2.79       154.32        27.19 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
      119.54        46.88        99.16        70.16        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-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       10.82        32.19        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 
       64.21         1.74        14.10        27.02        48.82        48.33 
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-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        9.57        11.77        64.93        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        54.28        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        98.01        79.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
      151.27        14.07        54.44        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
       36.62         6.94       118.36        27.16         2.63        61.61 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
       31.50        28.96        32.88        31.27        65.23        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       56.38         9.07        23.24        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
       18.15         4.96         1.12        27.19        20.91         3.95 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         6.58         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        0.39        74.07        44.75        68.58        55.20        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       60.79         1.71         1.94        36.39        15.58        35.64 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       17.88        17.06        40.21        38.66        27.02        33.11 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 
       18.38        27.91        24.89        21.47         3.81        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        7.76        66.51        13.38        11.77         9.73        14.20 
TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 
        9.99        13.91         0.39         0.39         5.46        30.35 
TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       27.45         0.10         0.99         0.43         0.99         1.45 
TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.85         0.10        17.49        26.89        17.00        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-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
       19.23        13.32        17.85        21.04         0.13         0.26 
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-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 
       85.12        34.36        56.65        21.11         3.58        12.23 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
       96.82        37.94        49.48        66.54        41.42         9.01 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 
       56.91        50.33        35.34        48.49         3.19        32.32 
TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ 
       35.90        26.83        11.77       102.67        66.61        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-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
        2.01        21.07         1.02         2.01         0.92        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       21.01        25.05         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       23.01         3.02         2.01        19.00        12.03         3.98 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 
       24.95         1.97        25.97        40.01         4.04        22.98 
TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
        5.03        54.08         4.01         6.64         6.94         8.02 
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-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7338 TCGA-77-7465 
       89.98        20.78         0.49        70.13         0.16        15.75 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
       86.76        53.95        37.81        12.59        53.92        17.72 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 
       11.54        27.39         6.97         9.63        35.90         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
      126.18       132.36         5.92        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
       38.86        11.97         6.41        36.53        34.95        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        14.07        16.87        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-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        0.72         7.76        14.63        13.94        12.59         0.10 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR 
       15.62        25.68        19.33        14.96        24.36        19.73 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       16.21        15.85        14.96         0.79        12.39        24.92 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
        9.50         2.93        11.77        14.07        20.22        22.62 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
       10.59         4.01         5.26         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
       11.70         4.01         5.03        26.63        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       17.69        49.87        57.07        18.31        17.46        16.57 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B 
        8.42        30.81        30.67        21.34        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       27.02        21.21        20.32        18.58        20.71        19.10 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       13.18        13.41        11.84         0.07        64.08         4.54 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO 
        1.22        13.74         4.21         2.89        37.22        30.58 
TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52S TCGA-O2-A5IB 
       22.78        65.49        16.80         0.43        12.72        11.18 
TCGA-XC-AA0X 
        0.20 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.39               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            174.08             154.32 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            22.735             18.150 
[1] "0.4 - 174.1 (22.7)" "0.0 - 154.3 (18.1)"
[1] "hr=" "1.4"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         2       15       40        1        16        28
  14Q GAIN WILD-TYPE       0       72      111        1        47        64
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  14Q GAIN MUTATED           1         20          3        2
  14Q GAIN WILD-TYPE         2         42         18        5
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 15                 72
  STAGE IB                 40                111
  STAGE II                  1                  1
  STAGE IIA                16                 47
  STAGE IIB                28                 64
  STAGE III                 1                  2
  STAGE IIIA               20                 42
  STAGE IIIB                3                 18
  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    19  82  23   4
  14Q GAIN WILD-TYPE  92 208  46  19
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               19                 92
  T2               82                208
  T3               23                 46
  T4                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                  N0  N1  N2  N3
  14Q GAIN MUTATED    83  30  14   0
  14Q GAIN WILD-TYPE 229 101  25   5
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               83                229
  N1               30                101
  N2               14                 25
  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   106   2
  14Q GAIN WILD-TYPE 298   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    106    2
  14Q GAIN WILD-TYPE  298    5
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0              106                298
  1                2                  5
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    33  95
  14Q GAIN WILD-TYPE  94 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     33   95
  14Q GAIN WILD-TYPE   94  271
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               33                 94
  MALE                 95                271
[1] 2 2
[1] FALSE
D26V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                       4
  14Q GAIN WILD-TYPE                                    11
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                         0
  14Q GAIN WILD-TYPE                                       1
                    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                                                           123
  14Q GAIN WILD-TYPE                                                         347
D26V9, multiclass
                                                             clus
vv                                                            14Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG CLEAR CELL 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)              123
                                                             clus
vv                                                            14Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                347
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     3 125
  14Q GAIN WILD-TYPE  10 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3  125
  14Q GAIN WILD-TYPE   10  355
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 3                 10
  YES              125                355
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED   102   4   1   8
  14Q GAIN WILD-TYPE 292   8   3  14
D26V13, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0              102                292
  R1                4                  8
  R2                1                  3
  RX                8                 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
  14Q GAIN MUTATED       3                         9    83
  14Q GAIN WILD-TYPE     6                        22   257
D26V14, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                9                 22
  WHITE                                   83                257
[1] 3 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   3 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   72
  14Q GAIN WILD-TYPE    3  237
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  3
  NOT HISPANIC OR LATINO               72                237
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    61  40
  15Q GAIN WILD-TYPE 220 156
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               101                376 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                40                156 
$`15Q GAIN MUTATED`
TCGA-18-3410 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-21-1077 
        4.80        23.54        36.07        86.96         6.18        34.78 
TCGA-21-1079 TCGA-21-1082 TCGA-21-5786 TCGA-22-4593 TCGA-22-4604 TCGA-22-4605 
       31.73       119.80        33.93        35.08        13.12        32.02 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5482 TCGA-22-5483 TCGA-33-4538 TCGA-33-4566 
       64.93        14.63        11.74        18.84        98.01       174.08 
TCGA-33-4583 TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5240 
      151.27         2.63        28.96        31.27        65.23        12.00 
TCGA-34-8455 TCGA-37-3792 TCGA-39-5037 TCGA-43-3394 TCGA-43-6770 TCGA-43-A475 
        4.04         0.39        35.70        27.02        21.47         9.73 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-8308 TCGA-56-A5DR TCGA-58-8391 
        0.43         1.45         0.85        17.00         0.13        71.24 
TCGA-58-8393 TCGA-58-A46K TCGA-60-2695 TCGA-60-2696 TCGA-60-2706 TCGA-60-2710 
       34.78        34.36        21.11         3.58        92.71        66.54 
TCGA-60-2711 TCGA-60-2719 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MI 
       41.42        42.64        29.85        23.57        26.83        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-77-7140 
        7.07        23.01        19.00         3.02         2.73        20.78 
TCGA-77-7141 TCGA-77-7463 TCGA-77-7465 TCGA-77-8133 TCGA-77-8136 TCGA-77-8150 
        0.49        46.78        15.75        53.92        39.09        54.41 
TCGA-77-A5G1 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7844 TCGA-85-7950 
      132.36        27.62        12.99         6.41        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         0.10        19.33        14.96 
TCGA-85-A50Z TCGA-85-A510 TCGA-90-7769 TCGA-90-A59Q TCGA-92-7341 TCGA-94-7943 
       16.21        15.85        11.77        10.59         3.48        11.70 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-98-8020 TCGA-98-A538 TCGA-98-A53B 
       16.14        17.69        57.07         2.76        27.16         2.01 
TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A7XE 
       16.11        13.18        64.08        29.75         0.43 

$`15Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       92.15        31.99         1.64         2.79       154.32        49.94 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
       27.19       119.54        46.88        99.16        70.16        60.89 
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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       41.69        10.82        32.19        21.99         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
        4.31        64.21         1.74        14.10        27.02        48.82 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       20.48        48.33        24.13         0.56        38.17        34.75 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 
       19.30         9.57        11.77        31.73        63.55        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 
        0.79        54.28        71.34        79.20        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 
       56.32        16.64        22.06         7.63       133.74        79.53 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      103.53        14.07        54.44         1.55        19.76        27.02 
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-34-2604 TCGA-34-2608 TCGA-34-5232 
      118.36        27.16        61.61        31.50        32.88        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       56.38         9.07        23.24        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        4.96         1.12        27.19        26.43        20.91         3.95 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         6.58         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        0.39         3.39        47.80        74.07        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        70.03        60.79         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 
       27.39        36.39        15.58        35.64        17.88        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       40.21        22.49        38.66        33.11        18.38        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
       12.36        24.89         5.46         3.81        19.59         7.76 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U 
       66.51        13.38        11.77         2.93        11.61        14.20 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       12.03         9.99        10.65        13.91         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
       29.95        28.34         5.46        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
       28.96         0.10        18.25         2.04         0.62         0.99 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        0.99         1.32         6.51         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
       26.89        14.07         1.35        16.77         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.18        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS 
       19.23        13.32        17.85        21.04        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 
        2.76         0.03        13.25        13.55        29.95        16.47 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 
       85.12        56.65        35.24        29.92        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 
       96.82        37.94        21.93        80.45        49.48         9.01 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 
       56.91        50.33        35.34        48.49         3.19        32.32 
TCGA-60-2723 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ 
       35.90        11.77       102.67        70.62        66.61        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-A5MU TCGA-63-A5MW TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       25.41        53.88        16.96         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-66-2768 TCGA-66-2777 TCGA-66-2778 
        0.99         2.01         1.02         2.01         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-68-7756 TCGA-68-7757 
       10.06        54.08         4.01        49.05         6.64         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
        8.02        13.35        16.18        14.73        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        89.98        42.28        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
      106.95         0.16         6.51        86.76        53.95        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       82.92        12.59        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         9.63        65.49        35.90         0.33 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
      126.18       117.57        22.29         5.92        42.41        42.08 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 
       30.81        38.86         9.67        11.97        36.53        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        14.07 
TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8353 TCGA-85-8355 
       16.87         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 
        0.72        14.63        13.94        12.59        15.62        25.68 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A511 
       17.72        24.36        18.18        19.73        12.56        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        0.79        12.39         3.65        24.92         9.50         2.93 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 
       14.07        20.22        22.62         2.70         4.01         5.26 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        2.30        21.04         0.16         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       14.14        49.87        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A 
        8.42        30.81        30.67        21.34         3.88        18.15 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       27.02        21.21        20.32        18.58        20.71        19.10 
TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG 
       12.89        13.41        11.84         0.07         4.54        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
        1.22        45.37        13.74         4.21         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       37.22        30.58        24.00        14.73        22.78        83.57 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       65.49         3.65        16.80        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89         8.58        11.18         0.20 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.10               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            174.08             154.32 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             21.11              18.66 
[1] "0.1 - 174.1 (21.1)" "0.0 - 154.3 (18.7)"
[1] "hr=" "1.2"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         0        9       31        0        18        22
  15Q GAIN WILD-TYPE       2       78      120        2        45        70
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  15Q GAIN MUTATED           0         15          4        3
  15Q GAIN WILD-TYPE         3         47         17        4
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  9                 78
  STAGE IB                 31                120
  STAGE II                  0                  2
  STAGE IIA                18                 45
  STAGE IIB                22                 70
  STAGE III                 0                  3
  STAGE IIIA               15                 47
  STAGE IIIB                4                 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
  15Q GAIN MUTATED    16  66  16   5
  15Q GAIN WILD-TYPE  95 224  53  18
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               16                 95
  T2               66                224
  T3               16                 53
  T4                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                  N0  N1  N2  N3
  15Q GAIN MUTATED    55  38   7   1
  15Q GAIN WILD-TYPE 257  93  32   4
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               55                257
  N1               38                 93
  N2                7                 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    89   3
  15Q GAIN WILD-TYPE 315   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     89    3
  15Q GAIN WILD-TYPE  315    4
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               89                315
  1                3                  4
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    21  82
  15Q GAIN WILD-TYPE 106 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     21   82
  15Q GAIN WILD-TYPE  106  284
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               21                106
  MALE                 82                284
[1] 2 2
[1] FALSE
D27V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                       4
  15Q GAIN WILD-TYPE                                    11
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                         1
  15Q GAIN WILD-TYPE                                       0
                    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                                                            97
  15Q GAIN WILD-TYPE                                                         373
D27V9, multiclass
                                                             clus
vv                                                            15Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               97
                                                             clus
vv                                                            15Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                373
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2 101
  15Q GAIN WILD-TYPE  11 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2  101
  15Q GAIN WILD-TYPE   11  379
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 2                 11
  YES              101                379
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    86   3   0   6
  15Q GAIN WILD-TYPE 308   9   4  16
D27V13, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               86                308
  R1                3                  9
  R2                0                  4
  RX                6                 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
  15Q GAIN MUTATED       1                         6    74
  15Q GAIN WILD-TYPE     8                        25   266
D27V14, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                6                 25
  WHITE                                   74                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"
D27V15, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  70
  15Q GAIN WILD-TYPE   7 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   70
  15Q GAIN WILD-TYPE    7  239
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               70                239
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    46  33
  16P GAIN WILD-TYPE 235 163
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                79                398 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                33                163 
$`16P GAIN MUTATED`
TCGA-18-3412 TCGA-18-3416 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1081 
       11.34        31.99        27.19        46.88        99.16         9.34 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5787 TCGA-22-1011 TCGA-22-1017 TCGA-22-4593 
       43.23        88.11        10.82         1.74        48.82        35.08 
TCGA-33-4532 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-34-2604 
        7.63       174.08       151.27        14.07        54.44        31.50 
TCGA-34-5240 TCGA-34-5241 TCGA-34-7107 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4135 
       12.00        16.93         1.12        26.43        20.91         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5034 TCGA-39-5036 TCGA-43-2576 TCGA-43-2578 
        0.39         3.39        36.39        35.64        40.21        22.49 
TCGA-43-5668 TCGA-43-A56V TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 TCGA-56-7222 
       18.38        12.03         8.75        28.96         2.04         0.43 
TCGA-56-7223 TCGA-56-8304 TCGA-56-8504 TCGA-56-A4BW TCGA-60-2706 TCGA-60-2722 
        0.99         3.48        16.77        19.23        92.71        29.85 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MV TCGA-66-2737 TCGA-66-2756 TCGA-66-2767 
       26.83        11.77        36.16         2.01         0.99         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2791 TCGA-66-2793 TCGA-77-7465 TCGA-77-8009 
        2.01        23.01         5.03        10.06        15.75        53.95 
TCGA-77-8139 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5GA TCGA-85-6175 TCGA-85-6560 
      104.09        54.41       132.36        42.08         9.67        11.97 
TCGA-85-7843 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 TCGA-85-A4JB 
        1.15        16.87        34.52         0.76        22.45        17.72 
TCGA-85-A510 TCGA-90-A59Q TCGA-92-7341 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-98-8020 
       15.85        10.59         3.48        14.14        16.14         2.76 
TCGA-98-8022 TCGA-98-A53J TCGA-J1-A4AH TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ 
       30.67        20.71        19.10        39.85        30.58        14.73 
TCGA-NK-A5CX 
        3.65 

$`16P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
       23.54        92.15        36.07         1.64        86.96         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 
        2.79       154.32        49.94       119.54        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 
       34.78        15.58        31.73       122.43       119.80        31.63 
TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       41.69        33.93        32.19        21.99         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
        4.31        64.21        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-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        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        54.28        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-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4589 
       22.06       133.74        98.01        79.53       103.53         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       19.76        27.02         4.70         0.30        36.62         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-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       28.96        32.88        31.27        65.23        67.79        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 
        9.07        23.24        30.94        18.15         4.96        27.19 
TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
        4.04         3.95         0.43         0.39         6.58         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        7.46         7.82        47.80        74.07        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        70.03        60.79         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2581 
       27.39        15.58        35.70        17.88        17.06        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       27.02        33.11        27.91        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
        5.46         3.81        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 
       11.77         2.93        11.61         9.73        14.20         9.99 
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-56-6546 
        5.46        30.35        27.45         0.10        18.25         0.62 
TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.99         1.45         1.32         0.85         6.51         0.10 
TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
       17.49        26.89        17.00        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         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       20.94        13.32        17.85        21.04        18.74         0.13 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26         2.76         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-60-2696 TCGA-60-2697 TCGA-60-2698 
       35.24        29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       41.42         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-63-A5MB 
       42.64         3.19        32.32        35.90        23.57       102.67 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
       70.62        66.61        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-A5MU 
       11.34        25.28        89.29        78.28        16.37        25.41 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
       53.88        34.59        16.96        43.10        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-66-2766 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
        0.99         2.01         1.02         7.07        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-66-2792 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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
        6.94         8.02        13.35        16.18        14.73        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 
       73.12        75.09        23.28        11.18        89.98        20.78 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        0.49        42.28        70.13       106.95         0.16        46.78 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        6.51        86.76        37.81        82.92        12.59        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       39.09        17.72        11.54        26.40        27.39         6.97 
TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 
        9.63        65.49        35.90         0.33       126.18       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
       22.29         5.92        42.41        30.81        27.62        38.86 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       12.99         6.41        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1.38        29.95        18.94        25.15        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
       31.56        14.07        10.09        13.22        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         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       13.94        12.59         0.10        15.62        25.68        19.33 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       14.96        24.36        18.18        19.73        12.56        16.21 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       14.96         0.79        12.39         3.65        24.92         9.50 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 
        2.93        11.77        14.07        20.22        22.62         2.70 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        4.01         5.26         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
        4.01         5.03        26.63        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       18.31        17.46        19.36        16.57         8.42        30.81 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       21.34        27.16         3.88        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       21.21        20.32        18.58        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       13.41        11.84         0.07        64.08         4.54        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
        1.22        45.37        13.74         4.21         2.89        37.22 
TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 
       24.00        29.75        22.78        83.57        65.49        16.80 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
        0.43        33.07         3.72        12.72        43.89         8.58 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.39               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            174.08             154.32 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            16.930             19.475 
[1] "0.4 - 174.1 (16.9)" "0.0 - 154.3 (19.5)"
[1] "hr=" "1"  
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         0       13       22        1        15        13
  16P GAIN WILD-TYPE       2       74      129        1        48        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  16P GAIN MUTATED           0         12          5        0
  16P GAIN WILD-TYPE         3         50         16        7
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 13                 74
  STAGE IB                 22                129
  STAGE II                  1                  1
  STAGE IIA                15                 48
  STAGE IIB                13                 79
  STAGE III                 0                  3
  STAGE IIIA               12                 50
  STAGE IIIB                5                 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
  16P GAIN MUTATED    16  52  12   2
  16P GAIN WILD-TYPE  95 238  57  21
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               16                 95
  T2               52                238
  T3               12                 57
  T4                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                  N0  N1  N2  N3
  16P GAIN MUTATED    49  24   7   2
  16P GAIN WILD-TYPE 263 107  32   3
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               49                263
  N1               24                107
  N2                7                 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    72   0
  16P GAIN WILD-TYPE 332   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     72    0
  16P GAIN WILD-TYPE  332    7
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               72                332
  1                0                  7
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    16  66
  16P GAIN WILD-TYPE 111 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     16   66
  16P GAIN WILD-TYPE  111  300
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               16                111
  MALE                 66                300
[1] 2 2
[1] FALSE
D28V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                       1
  16P GAIN WILD-TYPE                                    14
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                         1
  16P GAIN WILD-TYPE                                       0
                    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                                                            78
  16P GAIN WILD-TYPE                                                         392
D28V9, multiclass
                                                             clus
vv                                                            16P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG CLEAR CELL 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)               78
                                                             clus
vv                                                            16P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                392
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     2  80
  16P GAIN WILD-TYPE  11 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   80
  16P GAIN WILD-TYPE   11  400
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 2                 11
  YES               80                400
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, continuous
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    66   1   0   3
  16P GAIN WILD-TYPE 328  11   4  19
D28V13, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               66                328
  R1                1                 11
  R2                0                  4
  RX                3                 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    61
  16P GAIN WILD-TYPE     7                        28   279
D28V14, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                   61                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"
D28V15, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  57
  16P GAIN WILD-TYPE   7 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   57
  16P GAIN WILD-TYPE    7  252
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               57                252
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    45  33
  16Q GAIN WILD-TYPE 236 163
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                78                399 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                33                163 
$`16Q GAIN MUTATED`
TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 
       11.34        23.54        31.99        27.19        46.88        99.16 
TCGA-21-1079 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-1011 TCGA-22-1017 
       31.73        88.11        33.93        10.82         1.74        48.82 
TCGA-22-4593 TCGA-33-4532 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-AASD 
       35.08         7.63       174.08       151.27        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        20.91         7.82         6.81 
TCGA-37-4141 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-5668 TCGA-43-6143 
        0.39        35.64        35.70        40.21        18.38        12.36 
TCGA-43-A475 TCGA-43-A56V TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 TCGA-56-7223 
        9.73        12.03         8.75        28.96         2.04         0.99 
TCGA-56-8304 TCGA-56-8504 TCGA-56-A4BW TCGA-58-A46K TCGA-60-2706 TCGA-60-2708 
        3.48        16.77        19.23        34.36        92.71        80.45 
TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MV TCGA-66-2737 TCGA-66-2756 
       29.85        26.83        11.77        36.16         2.01         0.99 
TCGA-66-2768 TCGA-66-2781 TCGA-66-2791 TCGA-77-7465 TCGA-77-8009 TCGA-77-A5G1 
        2.01         3.98         5.03        15.75        53.95       132.36 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-7843 TCGA-85-8072 
       42.08        27.62         9.67        11.97         1.15        16.87 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-A510 
       34.52        10.09         0.76        22.45         5.29        15.85 
TCGA-85-A53L TCGA-90-A59Q TCGA-92-7341 TCGA-98-8020 TCGA-98-8022 TCGA-98-A53B 
       12.39        10.59         3.48         2.76        30.67         2.01 
TCGA-98-A53J TCGA-J1-A4AH TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HM TCGA-NK-A5CX 
       20.71        19.10        13.18        13.41        39.85         3.65 

$`16Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       92.15        36.07         1.64        86.96         6.18         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-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       15.58       122.43         9.34       119.80        43.23        31.63 
TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       41.69        32.19        21.99         7.33        14.93         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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
        9.57        11.77        31.73        64.93        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        54.28        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       18.84        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 
      133.74        98.01        79.53       103.53        14.07         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       19.76        27.02         4.70         0.30        36.62         6.94 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
       44.19       118.36        27.16         2.63        61.61        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       28.96        32.88        31.27        65.23        67.79        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
        9.07        23.24        12.00        30.94        18.15         4.96 
TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       27.19         4.04         3.95         0.43         0.39         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        8.12         7.46         3.39        47.80        74.07        44.75 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        70.03        60.79         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 
        1.94        27.39        36.39        15.58        17.88        17.06 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
       22.49        38.66        27.02        33.11        27.91        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
       21.47         5.46         3.81        19.59         7.76        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-46-3768 
       13.38        11.77         2.93        11.61        14.20         9.99 
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-56-6546 
        5.46        30.35        27.45         0.10        18.25         0.62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
        0.99         0.43         1.45         1.32         0.85         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 
        0.10        17.49        26.89        17.00        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         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       15.81        20.94        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         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-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 
       35.24        29.92        21.11         3.58        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       96.82        37.94        21.93        49.48        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
        9.01        56.91        50.33        35.34        48.49        42.64 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-63-A5MB TCGA-63-A5MG 
        3.19        32.32        35.90        23.57       102.67        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       66.61        58.65        59.97        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW 
       25.28        89.29        78.28        16.37        25.41        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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        6.64         6.94         8.02        13.35        16.18        14.73 
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        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       20.78         0.49        42.28        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
       46.78         6.51        86.76        37.81        82.92        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         9.63        54.41        65.49        35.90 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        0.33       126.18       117.57        22.29         5.92        42.41 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       30.81        38.86        12.99         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-85-8288 TCGA-85-8351 
       19.04        24.13        31.56        14.07        13.22        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         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       13.94        12.59         0.10        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       17.72        14.96        24.36        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       16.21        14.96         0.79         3.65        24.92         9.50 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 
        2.93        11.77        14.07        20.22        22.62         2.70 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        4.01         5.26         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        4.01         5.03        26.63        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       49.87        57.07        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
        8.42        30.81        21.34        27.16         3.88        18.15 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 
       27.02        21.21        20.32        18.58        12.89        16.11 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       11.84         0.07        64.08         4.54        51.78         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO 
       45.37        13.74         4.21         2.89        37.22        30.58 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       24.00        14.73        29.75        22.78        83.57        65.49 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       16.80         0.43        33.07         3.72        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        8.58        11.18         0.20 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.39               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            174.08             154.32 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             16.90              19.36 
[1] "0.4 - 174.1 (16.9)" "0.0 - 154.3 (19.4)"
[1] "hr=" "1"  
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0       12       24        1        17        12
  16Q GAIN WILD-TYPE       2       75      127        1        46        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  16Q GAIN MUTATED           0         12          4        1
  16Q GAIN WILD-TYPE         3         50         17        6
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 12                 75
  STAGE IB                 24                127
  STAGE II                  1                  1
  STAGE IIA                17                 46
  STAGE IIB                12                 80
  STAGE III                 0                  3
  STAGE IIIA               12                 50
  STAGE IIIB                4                 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
  16Q GAIN MUTATED    16  52  11   4
  16Q GAIN WILD-TYPE  95 238  58  19
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               16                 95
  T2               52                238
  T3               11                 58
  T4                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                  N0  N1  N2  N3
  16Q GAIN MUTATED    51  26   5   1
  16Q GAIN WILD-TYPE 261 105  34   4
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               51                261
  N1               26                105
  N2                5                 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    71   1
  16Q GAIN WILD-TYPE 333   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     71    1
  16Q GAIN WILD-TYPE  333    6
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               71                333
  1                1                  6
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    12  71
  16Q GAIN WILD-TYPE 115 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     12   71
  16Q GAIN WILD-TYPE  115  295
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               12                115
  MALE                 71                295
[1] 2 2
[1] FALSE
D29V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                       2
  16Q GAIN WILD-TYPE                                    13
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                         1
  16Q GAIN WILD-TYPE                                       0
                    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                                                            78
  16Q GAIN WILD-TYPE                                                         392
D29V9, multiclass
                                                             clus
vv                                                            16Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG CLEAR CELL 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)               78
                                                             clus
vv                                                            16Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                392
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2  81
  16Q GAIN WILD-TYPE  11 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   81
  16Q GAIN WILD-TYPE   11  399
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 2                 11
  YES               81                399
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    70   3   0   3
  16Q GAIN WILD-TYPE 324   9   4  19
D29V13, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               70                324
  R1                3                  9
  R2                0                  4
  RX                3                 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    60
  16Q GAIN WILD-TYPE     5                        26   280
D29V14, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                5                 26
  WHITE                                   60                280
[1] 3 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  62
  16Q GAIN WILD-TYPE   7 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   62
  16Q GAIN WILD-TYPE    7  247
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               62                247
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    37  28
  17P GAIN WILD-TYPE 244 168
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                65                412 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                28                168 
$`17P GAIN MUTATED`
TCGA-18-3412 TCGA-18-3417 TCGA-21-1071 TCGA-21-1072 TCGA-22-1017 TCGA-22-4593 
       11.34        36.07        46.88        99.16        48.82        35.08 
TCGA-22-4601 TCGA-22-4613 TCGA-22-5474 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 
       34.75        11.77        14.63         7.63        98.01       103.53 
TCGA-33-AASD TCGA-34-2596 TCGA-34-5240 TCGA-34-5241 TCGA-43-2578 TCGA-43-7657 
      110.99         2.63        12.00        16.93        22.49         7.76 
TCGA-43-8118 TCGA-46-6025 TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 TCGA-56-8308 
        2.93        10.65         0.43         0.85         6.51        17.00 
TCGA-56-8504 TCGA-58-8391 TCGA-58-A46K TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5ML 
       16.77        71.24        34.36        11.77       102.67        45.57 
TCGA-63-A5MU TCGA-66-2756 TCGA-66-2770 TCGA-66-2787 TCGA-66-2792 TCGA-68-8250 
       25.41         0.99        23.01        40.01        30.02         8.02 
TCGA-68-8251 TCGA-77-7142 TCGA-77-8156 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-7843 
       13.35        42.28         0.33        42.08        27.62         1.15 
TCGA-85-7950 TCGA-85-8277 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       18.94        10.09        22.45         5.29         3.09        32.71 
TCGA-85-8664 TCGA-85-A4JC TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE 
        0.10        14.96        15.85         3.65        11.77        22.62 
TCGA-92-7340 TCGA-94-7557 TCGA-94-7943 TCGA-96-8169 TCGA-98-8020 TCGA-98-A53I 
        2.70         0.16        11.70        18.31         2.76        18.58 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HL 
       19.10        16.11        11.84         1.22         2.89 

$`17P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
       23.54        92.15        31.99         1.64        86.96         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1075 
        2.79       154.32        49.94        27.19       119.54        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-21-1083 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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       10.82        32.19        21.99         7.33        14.93         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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
        9.57        31.73        64.93        63.55        44.25         0.79 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       54.28        71.34        79.20        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4547 
       62.86        56.32        16.64        22.06       133.74        79.53 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
      174.08       151.27        14.07        54.44         1.55        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI 
       27.02         4.70         0.30        36.62         6.94        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
      118.36        27.16        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.27        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       30.94        18.15         4.96         1.12        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       26.43        20.91         3.95         0.43         0.39         6.58 
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-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
       47.80        74.07        44.75        68.58        55.20        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       60.79         1.71        24.33         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
       15.58        35.64        35.70        17.88        17.06        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
       38.66        27.02        33.11        18.38        27.91        12.36 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 
       24.89        21.47         5.46         3.81        19.59        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
       13.38        11.77        11.61         9.73        14.20        12.03 
TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        9.99        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         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 
       18.25         2.04         0.62         0.99         0.99         1.45 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        1.32         0.10        17.49         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         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
       20.25        15.81        20.94        19.23        13.32        17.85 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       21.04        18.74         0.13         0.26         2.76         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-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 
       56.65        35.24        29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
       49.48        66.54        41.42         9.01        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
       35.34        48.49        42.64         3.19        32.32        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       35.90        23.57        26.83        70.62        66.61        58.65 
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-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-66-2767 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-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 
       25.97        22.98         4.04        22.98         5.03        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-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       16.18        14.73        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       11.18        89.98        20.78         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        15.75         6.51        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       37.81        82.92        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         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       54.41        65.49        35.90       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 
       22.29         5.92        42.41        30.81        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       11.97        12.99         6.41        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
       32.91         1.38        29.95        25.15        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
       31.56        14.07        16.87        34.52         0.76        13.22 
TCGA-85-8351 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       16.77         2.01         0.72         7.76        14.63        13.94 
TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA 
       12.59        15.62        25.68        19.33        17.72        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 
       18.18        19.73        12.56        16.21        14.96         0.79 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
       12.39        24.92         9.50         2.93        14.07        20.22 
TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
       10.59         3.48         4.01         5.26         2.30        21.04 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        4.01         5.03        26.63        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
       49.87        57.07        17.46        19.36        16.57         8.42 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
       30.81        30.67        21.34        27.16         3.88        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 
        2.01        27.02        21.21        20.32        20.71        12.89 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       13.18        13.41         0.07        64.08         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO 
       45.37        13.74         4.21        39.85        37.22        30.58 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       24.00        14.73        29.75        22.78        83.57        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
        3.65        16.80         0.43        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89         8.58        11.18         0.20 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.10               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            110.99             174.08 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            15.850             20.235 
[1] "0.1 - 111.0 (15.8)" "0.0 - 174.1 (20.2)"
[1] "hr=" "1.2"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         0       14       19        0        12        10
  17P GAIN WILD-TYPE       2       73      132        2        51        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  17P GAIN MUTATED           0          8          1        1
  17P GAIN WILD-TYPE         3         54         20        6
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 14                 73
  STAGE IB                 19                132
  STAGE II                  0                  2
  STAGE IIA                12                 51
  STAGE IIB                10                 82
  STAGE III                 0                  3
  STAGE IIIA                8                 54
  STAGE IIIB                1                 20
  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  44   6   2
  17P GAIN WILD-TYPE  97 246  63  21
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               14                 97
  T2               44                246
  T3                6                 63
  T4                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                  N0  N1  N2  N3
  17P GAIN MUTATED    43  18   4   0
  17P GAIN WILD-TYPE 269 113  35   5
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               43                269
  N1               18                113
  N2                4                 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"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    53   1
  17P GAIN WILD-TYPE 351   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     53    1
  17P GAIN WILD-TYPE  351    6
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               53                351
  1                1                  6
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    13  53
  17P GAIN WILD-TYPE 114 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     13   53
  17P GAIN WILD-TYPE  114  313
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               13                114
  MALE                 53                313
[1] 2 2
[1] FALSE
D30V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED                                       3
  17P GAIN WILD-TYPE                                    12
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED                                         0
  17P GAIN WILD-TYPE                                       1
                    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                                                            62
  17P GAIN WILD-TYPE                                                         408
D30V9, multiclass
                                                             clus
vv                                                            17P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG CLEAR CELL 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)               62
                                                             clus
vv                                                            17P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                408
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  66
  17P GAIN WILD-TYPE  13 414
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   66
  17P GAIN WILD-TYPE   13  414
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                 13
  YES               66                414
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, continuous
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    49   3   0   3
  17P GAIN WILD-TYPE 345   9   4  19
D30V13, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               49                345
  R1                3                  9
  R2                0                  4
  RX                3                 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                         4    49
  17P GAIN WILD-TYPE     8                        27   291
D30V14, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                4                 27
  WHITE                                   49                291
[1] 3 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   6 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2   45
  17P GAIN WILD-TYPE    6  264
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               45                264
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    91  60
  17Q GAIN WILD-TYPE 190 136
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               151                326 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                60                136 
$`17Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 TCGA-21-1071 TCGA-21-1072 
        7.46       117.57        11.34        36.07        46.88        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
       70.16        34.78       119.80        43.23        33.93        10.82 
TCGA-22-1012 TCGA-22-1017 TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       14.10        48.82        35.08        38.17        34.75        13.12 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5483 
       11.77        31.73        63.55        14.63        44.25        18.84 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-33-AASJ 
        7.63        98.01       103.53        14.07        27.02       118.36 
TCGA-34-2596 TCGA-34-2604 TCGA-34-5231 TCGA-34-5240 TCGA-34-8456 TCGA-37-3792 
        2.63        31.50        65.23        12.00        26.43         0.39 
TCGA-37-4133 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5037 TCGA-43-2576 
        7.82        74.07        44.75        60.79        35.70        40.21 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-8118 TCGA-43-A475 TCGA-46-3768 
       22.49        18.38         7.76         2.93         9.73         9.99 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-52-7812 TCGA-56-1622 TCGA-56-7222 
       10.65        13.91         0.39        27.45        28.96         0.43 
TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8308 TCGA-56-8504 
        0.99         0.85         6.51         3.48        17.00        16.77 
TCGA-56-8629 TCGA-56-A4BX TCGA-58-8386 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46K 
       15.81        13.32         0.03        71.24        85.12        34.36 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2715 
       35.24        29.92        96.82        92.71        21.93        35.34 
TCGA-60-2722 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML 
       29.85        11.77       102.67        66.61        59.97        45.57 
TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2742 TCGA-66-2756 TCGA-66-2758 
       25.41        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-68-8250 
       40.01         5.03        30.02        10.06         2.73         8.02 
TCGA-68-8251 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 
       13.35        29.56        23.28        11.18         0.49        42.28 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8128 TCGA-77-8136 TCGA-77-8139 TCGA-77-8156 
       15.75         6.51        37.81        39.09       104.09         0.33 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6560 
      117.57        22.29         5.92        42.08        27.62        11.97 
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-A4JC 
        3.09        32.71         0.10        15.62        25.68        14.96 
TCGA-85-A4QR TCGA-85-A510 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
       19.73        15.85         2.93        11.77        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-8169 
       10.59         2.70         3.48        16.14        57.07        18.31 
TCGA-96-A4JK TCGA-98-8023 TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 
       19.36        21.34        18.58        20.71        19.10        16.11 
TCGA-MF-A522 TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A7XE 
       11.84         2.89        39.85        29.75        83.57         0.43 
TCGA-O2-A52N 
       33.07 

$`17Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
       12.20        75.75        79.46         4.80        23.54        92.15 
TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       31.99         1.64        86.96         6.18         2.79       154.32 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
       49.94        27.19       119.54        60.89        15.58        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI 
      122.43         9.34        31.63        88.11        41.69        32.19 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       21.99         7.33        14.93         4.31        64.21         1.74 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4605 
       27.02        20.48        48.33        24.13         0.56        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5472 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       19.30         9.57        64.93         0.79        54.28        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-22-A5C4 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 
       22.06       133.74        79.53       174.08       151.27        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
        1.55        19.76         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 
      110.99        44.19        27.16        61.61        28.96        32.88 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 
       31.27        67.79        56.38         9.07        23.24        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       30.94        18.15         4.96         1.12        27.19         4.04 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       20.91         3.95         0.43         6.58         8.12         7.46 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 
        6.81         0.39         3.39        47.80        68.58        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       70.03         1.71        24.33         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 
       15.58        35.64        17.88        17.06        38.66        27.02 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       33.11        27.91        12.36        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 
        3.81        19.59        66.51        13.38        11.77        11.61 
TCGA-43-A56U TCGA-43-A56V TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       14.20        12.03         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
       30.35         8.75         0.10        18.25         2.04         0.62 
TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 
        0.99         1.45         1.32         0.10        17.49        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         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
        9.93        20.25        20.94        19.23        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 
       18.74         0.13         0.26         2.76        13.25        13.55 
TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 
       29.95        16.47        34.78        56.65        21.11         3.58 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       12.23        10.22        37.94        80.45        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       41.42         9.01        56.91        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG 
        3.19        32.32        35.90        23.57        26.83        70.62 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       58.65        14.99        11.34        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 
       16.37        34.59        16.96        43.10         2.01         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 
        1.02         2.01         0.92        43.99        25.05         2.01 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 
        1.02         2.01         7.07        19.00        19.00        12.03 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 
       12.00        24.95         1.97        25.97        22.98         4.04 
TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 
       22.98        54.08         4.01        49.05         6.64         6.94 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7140 
       16.18        14.73        73.12        75.09        89.98        20.78 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8009 
       70.13       106.95         0.16        46.78        86.76        53.95 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 
       82.92        12.59        53.92        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         9.63        54.41        65.49        35.90 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 
      126.18       132.36        42.41        30.81        38.86         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       12.99         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        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8355 
       16.87        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 
        0.72         7.76        14.63        13.94        12.59        19.33 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
       17.72        24.36        18.18        12.56        16.21        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
        0.79        12.39         3.65        24.92         9.50        14.07 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        4.01         5.26         2.30        21.04         0.16        11.70 
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        49.87 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       17.46        16.57         8.42         2.76        30.81        30.67 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       27.16         3.88        18.15         2.01        27.02        21.21 
TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE 
       20.32        12.89        13.18        13.41         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        51.78         1.22        45.37        13.74         4.21 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CT 
       37.22        30.58        24.00        14.73        22.78        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
        3.65        16.80         3.72        12.72        43.89         8.58 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.03               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            119.80             174.08 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             20.71              18.84 
[1] "0.0 - 119.8 (20.7)" "0.1 - 174.1 (18.8)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         1       20       48        0        30        27
  17Q GAIN WILD-TYPE       1       67      103        2        33        65
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  17Q GAIN MUTATED           0         17          7        3
  17Q GAIN WILD-TYPE         3         45         14        4
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 20                 67
  STAGE IB                 48                103
  STAGE II                  0                  2
  STAGE IIA                30                 33
  STAGE IIB                27                 65
  STAGE III                 0                  3
  STAGE IIIA               17                 45
  STAGE IIIB                7                 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
  17Q GAIN MUTATED    26 108  14   6
  17Q GAIN WILD-TYPE  85 182  55  17
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               26                 85
  T2              108                182
  T3               14                 55
  T4                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                  N0  N1  N2  N3
  17Q GAIN MUTATED    88  51  12   2
  17Q GAIN WILD-TYPE 224  80  27   3
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               88                224
  N1               51                 80
  N2               12                 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   126   3
  17Q GAIN WILD-TYPE 278   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    126    3
  17Q GAIN WILD-TYPE  278    4
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0              126                278
  1                3                  4
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    25 129
  17Q GAIN WILD-TYPE 102 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     25  129
  17Q GAIN WILD-TYPE  102  237
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               25                102
  MALE                129                237
[1] 2 2
[1] FALSE
D31V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED                                       6
  17Q GAIN WILD-TYPE                                     9
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED                                         1
  17Q GAIN WILD-TYPE                                       0
                    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                                                           146
  17Q GAIN WILD-TYPE                                                         324
D31V9, multiclass
                                                             clus
vv                                                            17Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              146
                                                             clus
vv                                                            17Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                324
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4 150
  17Q GAIN WILD-TYPE   9 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4  150
  17Q GAIN WILD-TYPE    9  330
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 4                  9
  YES              150                330
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED   122   5   2   5
  17Q GAIN WILD-TYPE 272   7   2  17
D31V13, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0              122                272
  R1                5                  7
  R2                2                  2
  RX                5                 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   108
  17Q GAIN WILD-TYPE     7                        26   232
D31V14, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                5                 26
  WHITE                                  108                232
[1] 3 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  93
  17Q GAIN WILD-TYPE   4 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   93
  17Q GAIN WILD-TYPE    4  216
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               93                216
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    86  57
  18P GAIN WILD-TYPE 195 139
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               143                334 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                57                139 
$`18P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 TCGA-18-4083 TCGA-21-1075 
        7.46       117.57        11.34        31.99         6.18        70.16 
TCGA-21-1079 TCGA-21-1082 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 
       31.73       119.80        88.11        41.69        33.93         7.33 
TCGA-22-4591 TCGA-22-4595 TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 TCGA-22-5480 
       20.48        24.13        13.12        11.77        31.73        71.34 
TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4566 TCGA-33-4586 
       18.84        62.86        56.32         7.63       174.08        14.07 
TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-2604 TCGA-34-5231 TCGA-34-5236 
      110.99        44.19         2.63        31.50        65.23         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-37-3792 TCGA-37-4141 TCGA-39-5016 TCGA-39-5019 
       23.24        12.00         0.39         0.39        74.07        44.75 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 TCGA-39-5040 
       68.58        60.79        24.33        27.39        35.70        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-5670 TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 
       40.21        22.49        27.91        12.36         7.76        66.51 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-46-6026 TCGA-51-4081 TCGA-52-7811 
        2.93        11.61         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         0.99         1.32         6.51         3.48        14.07 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 
       20.94        13.32        17.85         0.13         0.26         0.03 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46N TCGA-60-2698 TCGA-60-2711 TCGA-60-2712 
       71.24        16.47        29.92        10.22        41.42         9.01 
TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MU 
       29.85        26.83        11.77        58.65        45.57        25.41 
TCGA-63-A5MW TCGA-66-2734 TCGA-66-2758 TCGA-66-2759 TCGA-66-2767 TCGA-66-2769 
       53.88        43.10        21.01        25.05         2.01         7.07 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2783 TCGA-66-2787 TCGA-66-2793 TCGA-66-2794 
       23.01         2.01        24.95        40.01        10.06        54.08 
TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-77-6845 TCGA-77-7335 TCGA-77-7463 
       49.05         2.73        14.73        23.28        70.13        46.78 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8143 TCGA-77-8150 
       15.75        53.95        37.81        82.92        26.40        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
       65.49         0.33       117.57        27.62        12.99         6.41 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
        1.15        29.95        19.04        31.56        14.07        34.52 
TCGA-85-8277 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 
       10.09         5.29         3.09        32.71         0.10        15.62 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A50M TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7769 
       19.33        17.72        12.56        15.85         3.65        11.77 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8064 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7545 
       22.62        10.59         5.26        14.14        16.14        57.07 
TCGA-98-8021 TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HI 
       30.81        18.58        19.10        12.89        16.11        45.37 
TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A5IB 
        2.89        14.73         3.65        33.07        11.18 

$`18P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
       12.20        75.75        79.46         4.80        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       36.07         1.64        86.96         2.79       154.32        49.94 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 
       27.19       119.54        46.88        99.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5787 
       15.58       122.43         9.34        43.23        31.63        10.82 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       32.19        21.99        14.93         4.31        64.21         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 
       14.10        27.02        48.82        35.08        48.33         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5472 
       38.17        34.75        32.02        19.30         9.57        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 
       63.55        14.63        44.25         0.79        54.28        79.20 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 
       11.74        30.12        16.64        22.06       133.74        98.01 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
       79.53       103.53       151.27        54.44         1.55        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ 
       27.02         4.70         0.30        36.62         6.94       118.36 
TCGA-33-AASL TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 
       27.16        61.61        28.96        32.88        31.27        67.79 
TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       56.38        16.93        30.94        18.15         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       27.19         4.04        26.43        20.91         3.95         0.43 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 
        6.58         8.12         7.46         7.82         6.81         3.39 
TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 
       47.80        55.20        70.03         1.71         1.94        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       15.58        35.64        17.88        38.66        27.02        33.11 
TCGA-43-5668 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       18.38        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
       13.38        11.77        14.20        12.03         9.99        10.65 
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-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
       28.96         0.10         2.04         0.62         0.99         0.43 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 
        1.45         0.85         0.10        17.49        26.89        17.00 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK 
        9.93        20.25        15.81        19.23        21.04        18.74 
TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J 
        2.76        13.25        13.55        29.95        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 
       34.36        56.65        35.24        21.11         3.58        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-60-2715 TCGA-60-2716 TCGA-60-2719 
       66.54        56.91        50.33        35.34        48.49        42.64 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-63-A5MB TCGA-63-A5MG 
        3.19        32.32        35.90        23.57       102.67        70.62 
TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       66.61        59.97        14.99        11.34        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2737 
       78.28        16.37        36.16        34.59        16.96         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-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 
       43.99         0.99         2.01         1.02         2.01        19.00 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 
        3.02        19.00        12.03         3.98        12.00         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-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
        4.01         6.64         6.94         8.02        13.35        16.18 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 
       29.56        73.12        75.09        11.18        89.98        20.78 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 
        0.49        42.28       106.95         0.16         6.51        86.76 
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-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       27.39         6.97         9.63        35.90       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH 
       22.29         5.92        42.41        42.08        30.81        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
        9.67        11.97        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 TCGA-85-8072 TCGA-85-8287 
        1.38        18.94        25.15        24.13        16.87         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       13.22        22.45        16.77         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA 
       14.63        13.94        12.59        25.68        14.96        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       18.18        19.73        16.21        14.96         0.79        12.39 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 
       24.92         9.50         2.93        14.07        20.22         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        3.48         4.01         2.30        21.04         0.16        11.70 
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        49.87        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 
       17.46        19.36        16.57         8.42         2.76        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       21.34        27.16         3.88        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       21.21        20.32        20.71        13.18        13.41        11.84 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ 
        0.07        64.08         4.54        51.78         1.22        13.74 
TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR 
        4.21        39.85        37.22        30.58        24.00        29.75 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q 
       22.78        83.57        65.49        16.80         0.43         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       12.72        43.89         8.58         0.20 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.03               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            174.08             154.32 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            19.100             19.115 
[1] "0.0 - 174.1 (19.1)" "0.1 - 154.3 (19.1)"
[1] "hr=" "1.1"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         1       23       45        0        24        24
  18P GAIN WILD-TYPE       1       64      106        2        39        68
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  18P GAIN MUTATED           1         22          8        1
  18P GAIN WILD-TYPE         2         40         13        6
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 23                 64
  STAGE IB                 45                106
  STAGE II                  0                  2
  STAGE IIA                24                 39
  STAGE IIB                24                 68
  STAGE III                 1                  2
  STAGE IIIA               22                 40
  STAGE IIIB                8                 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
  18P GAIN MUTATED    29  95  19   6
  18P GAIN WILD-TYPE  82 195  50  17
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               29                 82
  T2               95                195
  T3               19                 50
  T4                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                  N0  N1  N2  N3
  18P GAIN MUTATED    85  44  16   2
  18P GAIN WILD-TYPE 227  87  23   3
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               85                227
  N1               44                 87
  N2               16                 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"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   124   1
  18P GAIN WILD-TYPE 280   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    124    1
  18P GAIN WILD-TYPE  280    6
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0              124                280
  1                1                  6
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    34 115
  18P GAIN WILD-TYPE  93 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     34  115
  18P GAIN WILD-TYPE   93  251
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               34                 93
  MALE                115                251
[1] 2 2
[1] FALSE
D32V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                       4
  18P GAIN WILD-TYPE                                    11
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                         0
  18P GAIN WILD-TYPE                                       1
                    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                                                         326
D32V9, multiclass
                                                             clus
vv                                                            18P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG CLEAR CELL 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)              144
                                                             clus
vv                                                            18P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                326
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     7 142
  18P GAIN WILD-TYPE   6 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7  142
  18P GAIN WILD-TYPE    6  338
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 7                  6
  YES              142                338
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, continuous
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED   118   3   3   9
  18P GAIN WILD-TYPE 276   9   1  13
D32V13, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0              118                276
  R1                3                  9
  R2                3                  1
  RX                9                 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
  18P GAIN MUTATED       4                         3   110
  18P GAIN WILD-TYPE     5                        28   230
D32V14, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                  110                230
[1] 3 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   6 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   95
  18P GAIN WILD-TYPE    6  214
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               95                214
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    59  42
  18Q GAIN WILD-TYPE 222 154
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               101                376 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                42                154 
$`18Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-4083 TCGA-21-1075 TCGA-21-1082 TCGA-21-5783 
        7.46       117.57         6.18        70.16       119.80        88.11 
TCGA-21-5784 TCGA-22-1012 TCGA-22-4595 TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 
       41.69        14.10        24.13        13.12        11.77        31.73 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 
        0.79        71.34        79.20        18.84        62.86        56.32 
TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-34-2596 TCGA-34-2604 
        7.63       174.08       103.53        14.07         2.63        31.50 
TCGA-34-2609 TCGA-34-5236 TCGA-34-5239 TCGA-34-8456 TCGA-37-4141 TCGA-39-5019 
       31.27         9.07        23.24        26.43         0.39        44.75 
TCGA-39-5021 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 
       68.58        24.33        27.39        35.70        17.06        22.49 
TCGA-43-3920 TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-A475 
       33.11        12.36         7.76        66.51        13.38         9.73 
TCGA-46-6026 TCGA-51-4081 TCGA-52-7811 TCGA-56-5898 TCGA-56-7580 TCGA-56-7730 
       13.91        29.95         8.75        18.25         1.32         6.51 
TCGA-56-A49D TCGA-56-A4BX TCGA-58-8392 TCGA-58-A46N TCGA-60-2695 TCGA-60-2711 
       20.94        13.32        16.47        29.92        21.11        41.42 
TCGA-60-2712 TCGA-60-2722 TCGA-60-2725 TCGA-63-A5ML TCGA-66-2758 TCGA-66-2759 
        9.01        29.85        26.83        45.57        21.01        25.05 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2787 TCGA-66-2793 TCGA-66-2794 
        7.07        23.01         2.01        40.01        10.06        54.08 
TCGA-66-2800 TCGA-68-7755 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
       49.05         2.73        46.78        15.75        53.95        37.81 
TCGA-77-8143 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5GF TCGA-85-6561 
       26.40        54.41        65.49         0.33        27.62        12.99 
TCGA-85-6798 TCGA-85-7843 TCGA-85-7950 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 
        6.41         1.15        18.94        31.56        14.07        10.09 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A50M TCGA-90-A4EE 
        0.10        15.62        19.33        17.72        12.56        22.62 
TCGA-90-A59Q TCGA-92-8064 TCGA-96-7545 TCGA-98-8021 TCGA-98-A53I TCGA-J1-A4AH 
       10.59         5.26        57.07        30.81        18.58        19.10 
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-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 
       12.20        75.75        79.46         4.80        11.34        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       92.15        31.99        36.07         1.64        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
      154.32        49.94        27.19       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-21-A5DI TCGA-22-0940 
       43.23        31.63        33.93        10.82        32.19        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
        7.33        14.93         4.31        64.21         1.74        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       48.82        20.48        35.08        48.33         0.56        38.17 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5472 TCGA-22-5473 
       34.75        32.02        19.30         9.57        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 
       14.63        44.25        54.28        11.74        30.12        16.64 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 
       22.06       133.74        98.01        79.53       151.27        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
        1.55        19.76        27.02         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-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 
       28.96        32.88        65.23        67.79        56.38        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        30.94        18.15         4.96         1.12        27.19 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
        4.04        20.91         3.95         0.43         0.39         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 
        8.12         7.46         7.82         6.81         3.39        47.80 
TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
       74.07        55.20        70.03        60.79         1.71         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 
       36.39        15.58        35.64        17.88        40.21        38.66 
TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       27.02        18.38        27.91        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U 
        3.81        19.59        11.77         2.93        11.61        14.20 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
       12.03         9.99        10.65         0.39         0.39        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
        5.46        30.35        27.45        28.96         0.10         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
        0.62         0.99         0.43         0.99         1.45         0.85 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.10        17.49         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
        9.93        20.25        15.81        19.23        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       18.74         0.13         0.26         2.76         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-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       56.65        35.24         3.58        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-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       56.91        50.33        35.34        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG 
       32.32        35.90        23.57        11.77       102.67        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       66.61        58.65        59.97        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       89.29        78.28        16.37        25.41        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-66-2763 
        1.02         2.01         0.92         0.99        43.99         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 
        2.01         1.02         2.01         2.01        19.00         3.02 
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-66-2788 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-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
        4.01         6.64         6.94         8.02        13.35        16.18 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       14.73        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       89.98        20.78         0.49        42.28        70.13       106.95 
TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        0.16         6.51        86.76        82.92        12.59        53.92 
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-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        9.63        35.90       126.18       132.36       117.57        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 
        5.92        42.41        42.08        30.81        38.86         9.67 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
       11.97        36.53        34.95        31.30        32.91         1.38 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 
       29.95        25.15        19.04        24.13        16.87        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         0.72         7.76        14.63        13.94 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       12.59        25.68        14.96        24.36        18.18        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         0.79        12.39         3.65 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
       24.92         9.50         2.93        11.77        14.07        20.22 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        2.70         3.48         4.01         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
       11.70         4.01         5.03        26.63        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       17.69        49.87        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        8.42         2.76        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J 
       18.15         2.01        27.02        21.21        20.32        20.71 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       16.11        13.18        13.41         0.07        64.08         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM 
       51.78         1.22        45.37        13.74         4.21        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT 
       37.22        30.58        24.00        14.73        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       83.57        65.49        16.80         0.43        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       12.72        43.89         8.58         0.20 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.10               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            174.08             154.32 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             19.33              19.02 
[1] "0.1 - 174.1 (19.3)" "0.0 - 154.3 (19.0)"
[1] "hr=" "1"  
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         0       16       36        0        19        15
  18Q GAIN WILD-TYPE       2       71      115        2        44        77
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  18Q GAIN MUTATED           1         12          5        0
  18Q GAIN WILD-TYPE         2         50         16        7
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 16                 71
  STAGE IB                 36                115
  STAGE II                  0                  2
  STAGE IIA                19                 44
  STAGE IIB                15                 77
  STAGE III                 1                  2
  STAGE IIIA               12                 50
  STAGE IIIB                5                 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
  18Q GAIN MUTATED    21  70   8   5
  18Q GAIN WILD-TYPE  90 220  61  18
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               21                 90
  T2               70                220
  T3                8                 61
  T4                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                  N0  N1  N2  N3
  18Q GAIN MUTATED    62  31  10   0
  18Q GAIN WILD-TYPE 250 100  29   5
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               62                250
  N1               31                100
  N2               10                 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"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    91   0
  18Q GAIN WILD-TYPE 313   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     91    0
  18Q GAIN WILD-TYPE  313    7
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               91                313
  1                0                  7
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    24  80
  18Q GAIN WILD-TYPE 103 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     24   80
  18Q GAIN WILD-TYPE  103  286
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               24                103
  MALE                 80                286
[1] 2 2
[1] FALSE
D33V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED                                       3
  18Q GAIN WILD-TYPE                                    12
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED                                         0
  18Q GAIN WILD-TYPE                                       1
                    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                                                           101
  18Q GAIN WILD-TYPE                                                         369
D33V9, multiclass
                                                             clus
vv                                                            18Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG CLEAR CELL 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)              101
                                                             clus
vv                                                            18Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                369
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     6  98
  18Q GAIN WILD-TYPE   7 382
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6   98
  18Q GAIN WILD-TYPE    7  382
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 6                  7
  YES               98                382
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    85   3   2   3
  18Q GAIN WILD-TYPE 309   9   2  19
D33V13, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               85                309
  R1                3                  9
  R2                2                  2
  RX                3                 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
  18Q GAIN MUTATED       2                         1    78
  18Q GAIN WILD-TYPE     7                        30   262
D33V14, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                1                 30
  WHITE                                   78                262
[1] 3 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  65
  18Q GAIN WILD-TYPE   6 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   65
  18Q GAIN WILD-TYPE    6  244
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               65                244
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    63  44
  19P GAIN WILD-TYPE 218 152
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               107                370 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                44                152 
$`19P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3421 TCGA-21-5787 TCGA-22-1011 
        7.46         4.80       117.57        86.96        10.82         1.74 
TCGA-22-1012 TCGA-22-4593 TCGA-22-4595 TCGA-22-4604 TCGA-22-5471 TCGA-22-5474 
       14.10        35.08        24.13        13.12        31.73        14.63 
TCGA-22-5477 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-33-4533 TCGA-33-4538 
       44.25        79.20        18.84        62.86       133.74        98.01 
TCGA-33-4566 TCGA-33-4586 TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
      174.08        14.07       118.36         2.63        61.61        28.96 
TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-7107 TCGA-34-A5IX TCGA-39-5016 
       65.23        23.24        12.00         1.12        20.91        74.07 
TCGA-39-5019 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-6143 
       44.75        27.39        36.39        15.58        17.06        12.36 
TCGA-43-7657 TCGA-43-A475 TCGA-46-3768 TCGA-52-7809 TCGA-56-6546 TCGA-56-7580 
        7.76         9.73         9.99         5.46         0.62         1.32 
TCGA-56-7582 TCGA-56-8304 TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
        0.85         3.48        34.78        35.24        29.92        21.11 
TCGA-60-2704 TCGA-60-2708 TCGA-60-2712 TCGA-60-2719 TCGA-63-A5MB TCGA-63-A5MG 
       37.94        80.45         9.01        42.64       102.67        70.62 
TCGA-63-A5MH TCGA-63-A5ML TCGA-66-2763 TCGA-66-2770 TCGA-66-2777 TCGA-66-2787 
       66.61        45.57         0.99        23.01         2.01        40.01 
TCGA-66-2794 TCGA-66-2800 TCGA-68-8251 TCGA-68-A59J TCGA-77-6843 TCGA-77-7139 
       54.08        49.05        13.35        14.73        73.12        89.98 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8148 
        0.49        42.28        15.75        86.76        53.95         9.63 
TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
       54.41       132.36       117.57         5.92        42.41        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7843 TCGA-85-7950 
        9.67        12.99         6.41        36.53         1.15        18.94 
TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-A4CN TCGA-85-A4QR 
       10.09         3.09        32.71         0.72        19.33        19.73 
TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 
        3.65        11.77        22.62        10.59         2.70         5.26 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A53I TCGA-J1-A4AH TCGA-LA-A446 
       57.07        19.36         2.76        18.58        19.10        13.18 
TCGA-LA-A7SW TCGA-NC-A5HL TCGA-NC-A5HR TCGA-NK-A5CX TCGA-O2-A52W 
       13.41         2.89        29.75         3.65         8.58 

$`19P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       12.20        75.75        79.46        11.34        23.54        92.15 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       31.99        36.07         1.64         6.18         2.79       154.32 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
       49.94        27.19       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-21-1082 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-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       32.19        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       27.02        48.82        20.48        48.33         0.56        38.17 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 
       34.75        32.02        19.30         9.57        11.77        64.93 
TCGA-22-5473 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 
       63.55         0.79        54.28        71.34        11.74        30.12 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4582 
       56.32        16.64        22.06         7.63        79.53       103.53 
TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
      151.27        54.44         1.55        19.76        27.02         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-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       31.50        32.88        31.27        67.79        56.38         9.07 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 
       16.93        30.94        18.15         4.96        27.19         4.04 
TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       26.43         3.95         0.43         0.39         6.58         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        7.46         7.82         6.81         0.39         3.39        47.80 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        70.03        60.79         1.71        24.33 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 
        1.94        35.64        35.70        17.88        40.21        22.49 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
       38.66        27.02        33.11        18.38        27.91        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
       21.47         5.46         3.81        19.59        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 
       11.77         2.93        11.61        14.20        12.03        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 
       13.91         0.39         0.39        29.95        28.34        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         0.10        18.25         2.04 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 
        0.99         0.43         0.99         1.45         6.51         0.10 
TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
       17.49        26.89        17.00        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
       15.81        20.94        19.23        13.32        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       18.74         0.13         0.26         2.76         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-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 
       56.65         3.58        12.23        10.22        96.82        92.71 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
       21.93        49.48        66.54        41.42        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
       35.34        48.49         3.19        32.32        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM 
       23.57        26.83        11.77        58.65        59.97        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       11.34        25.28        89.29        78.28        16.37        25.41 
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-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       43.99        21.01        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-66-2782 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-66-2792 TCGA-66-2793 TCGA-66-2795 
        4.04        22.98         5.03        30.02        10.06         4.01 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6842 
        2.73         6.64         6.94         8.02        16.18        29.56 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7335 TCGA-77-7337 
       75.09        23.28        11.18        20.78        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        0.16        46.78         6.51        37.81        82.92        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-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       27.39         6.97        65.49        35.90         0.33       126.18 
TCGA-77-A5G6 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 
       22.29        42.08        30.81        38.86        11.97        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-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
       24.13        31.56        14.07        16.87        34.52         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8481 
       13.22        22.45        16.77         5.29         2.01         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z 
       17.72        14.96        24.36        18.18        12.56        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 
       15.85        14.96         0.79        12.39        24.92         9.50 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
        2.93        14.07        20.22         3.48         4.01         2.30 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
       21.04         0.16        11.70         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
       14.14        16.14        17.69        49.87        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       16.57         8.42        30.81        30.67        21.34        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        20.32 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       20.71        12.89        16.11        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        51.78         1.22        45.37        13.74         4.21 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
       39.85        37.22        30.58        24.00        14.73        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       83.57        65.49        16.80         0.43        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89        11.18         0.20 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.49               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            174.08             154.32 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             19.33              19.02 
[1] "0.5 - 174.1 (19.3)" "0.0 - 154.3 (19.0)"
[1] "hr=" "1.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         1       17       35        1        18        17
  19P GAIN WILD-TYPE       1       70      116        1        45        75
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  19P GAIN MUTATED           0         17          4        0
  19P GAIN WILD-TYPE         3         45         17        7
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 17                 70
  STAGE IB                 35                116
  STAGE II                  1                  1
  STAGE IIA                18                 45
  STAGE IIB                17                 75
  STAGE III                 0                  3
  STAGE IIIA               17                 45
  STAGE IIIB                4                 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
  19P GAIN MUTATED    20  70  16   4
  19P GAIN WILD-TYPE  91 220  53  19
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               20                 91
  T2               70                220
  T3               16                 53
  T4                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                  N0  N1  N2  N3
  19P GAIN MUTATED    66  35   8   0
  19P GAIN WILD-TYPE 246  96  31   5
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               66                246
  N1               35                 96
  N2                8                 31
  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    93   0
  19P GAIN WILD-TYPE 311   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     93    0
  19P GAIN WILD-TYPE  311    7
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               93                311
  1                0                  7
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    27  83
  19P GAIN WILD-TYPE 100 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     27   83
  19P GAIN WILD-TYPE  100  283
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               27                100
  MALE                 83                283
[1] 2 2
[1] FALSE
D34V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED                                       7
  19P GAIN WILD-TYPE                                     8
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED                                         0
  19P GAIN WILD-TYPE                                       1
                    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                                                           102
  19P GAIN WILD-TYPE                                                         368
D34V9, multiclass
                                                             clus
vv                                                            19P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG CLEAR CELL 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)              102
                                                             clus
vv                                                            19P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                368
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6 104
  19P GAIN WILD-TYPE   7 376
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6  104
  19P GAIN WILD-TYPE    7  376
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 6                  7
  YES              104                376
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, continuous
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    89   2   1   5
  19P GAIN WILD-TYPE 305  10   3  17
D34V13, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               89                305
  R1                2                 10
  R2                1                  3
  RX                5                 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
  19P GAIN MUTATED       2                         6    77
  19P GAIN WILD-TYPE     7                        25   263
D34V14, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                6                 25
  WHITE                                   77                263
[1] 3 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  66
  19P GAIN WILD-TYPE   6 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   66
  19P GAIN WILD-TYPE    6  243
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               66                243
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    86  67
  19Q GAIN WILD-TYPE 195 129
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               153                324 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                67                129 
$`19Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 
        7.46         4.80       117.57        36.07        86.96       119.54 
TCGA-21-1071 TCGA-21-1081 TCGA-21-5786 TCGA-21-5787 TCGA-22-1011 TCGA-22-1012 
       46.88         9.34        33.93        10.82         1.74        14.10 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-5477 
       35.08        24.13        38.17        34.75        13.12        44.25 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4533 TCGA-33-4538 
       79.20        18.84        30.12        62.86       133.74        98.01 
TCGA-33-4566 TCGA-33-4582 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI 
      174.08       103.53        19.76        27.02       110.99        44.19 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
        2.63        61.61        31.50        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 TCGA-34-A5IX 
       65.23        23.24        12.00        18.15         1.12        20.91 
TCGA-37-3792 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5029 TCGA-39-5031 
        0.39         3.39        74.07        44.75        24.33        27.39 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 TCGA-43-3920 TCGA-43-5668 
       36.39        15.58        17.88        17.06        33.11        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-7657 TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 
       27.91        12.36         7.76         9.73        12.03         9.99 
TCGA-52-7809 TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-7582 TCGA-56-8304 
        5.46         2.04         0.62         1.32         0.85         3.48 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A5DR TCGA-58-8393 TCGA-58-A46K 
       15.81        20.94        17.85         0.13        34.78        34.36 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2704 TCGA-60-2708 TCGA-60-2712 
       35.24        29.92        21.11        37.94        80.45         9.01 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH 
       42.64        29.85        35.90       102.67        70.62        66.61 
TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MV TCGA-66-2742 TCGA-66-2758 TCGA-66-2763 
       45.57        89.29        36.16        21.07        21.01         0.99 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2787 TCGA-66-2788 TCGA-66-2793 TCGA-66-2800 
       23.01         2.01        40.01        22.98        10.06        49.05 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-7138 
       13.35        16.18        14.73        29.56        73.12        11.18 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
        0.49        42.28        70.13        15.75        86.76        53.95 
TCGA-77-8130 TCGA-77-8138 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G1 
       82.92        17.72         6.97         9.63        54.41       132.36 
TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-7696 
      117.57         5.92        42.41        27.62         9.67        36.53 
TCGA-85-7699 TCGA-85-8350 TCGA-85-8353 TCGA-85-8354 TCGA-85-A4CN TCGA-85-A4QR 
       32.91        22.45         3.09        32.71        19.33        19.73 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE 
       12.56        15.85        12.39         3.65        11.77        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-A5I6 TCGA-96-7545 
       10.59         2.70         3.48         5.26        17.69        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-8022 TCGA-98-A53B TCGA-98-A53I TCGA-J1-A4AH 
       19.36         2.76        30.67         2.01        18.58        19.10 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CT 
       13.18        13.41         2.89        14.73        29.75        65.49 
TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52W 
        3.65         0.43         8.58 

$`19Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       12.20        75.75        79.46        11.34        23.54        92.15 
TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       31.99         1.64         6.18         2.79       154.32        49.94 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       27.19        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-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       41.69        32.19        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 
       64.21        27.02        48.82        20.48        48.33         0.56 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       32.02        19.30         9.57        11.77        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 
       63.55        14.63         0.79        54.28        71.34        11.74 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4583 
       56.32        16.64        22.06         7.63        79.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       14.07        54.44         1.55         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
        6.94       118.36        27.16        67.79        56.38         9.07 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       16.93        30.94         4.96        27.19         4.04        26.43 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        3.95         0.43         6.58         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        6.81         0.39        47.80        68.58        55.20        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
       60.79         1.71         1.94        35.64        35.70        40.21 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       22.49        38.66        27.02        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        3.81        19.59        66.51        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       11.61        14.20        10.65        13.91         0.39         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-56-5897 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
        0.10        18.25         0.99         0.43         0.99         1.45 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        6.51         0.10        17.49        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK 
        9.93        20.25        19.23        13.32        21.04        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26         2.76         0.03        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-60-2696 TCGA-60-2697 
       71.24        16.47        85.12        56.65         3.58        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-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
       41.42        56.91        50.33        35.34        48.49         3.19 
TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MI TCGA-63-A5MJ 
       32.32        23.57        26.83        11.77        58.65        59.97 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       14.99        11.34        25.28        78.28        16.37        25.41 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 
       53.88        34.59        16.96        43.10         2.01         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 
        1.02         2.01         0.92         0.99        43.99        25.05 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
        2.01         1.02         2.01         2.01         7.07        19.00 
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-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        1.97        25.97         4.04        22.98         5.03        30.02 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
       54.08         4.01         2.73         6.64         6.94         8.02 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7337 TCGA-77-7338 
       75.09        23.28        89.98        20.78       106.95         0.16 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       46.78         6.51        37.81        12.59        53.92        39.09 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 
      104.09        11.54        26.40        27.39        65.49        35.90 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH 
        0.33       126.18        22.29        42.08        30.81        38.86 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
       11.97        12.99         6.41        34.95        31.30         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        14.07        16.87        34.52        10.09         0.76 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       13.22        16.77         5.29         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A511 
       17.72        14.96        24.36        18.18        16.21        14.96 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
        0.79        24.92         9.50         2.93        14.07        20.22 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 
        4.01         2.30        21.04         0.16        11.70         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 TCGA-96-8169 
        5.03        26.63        14.14        16.14        49.87        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 
       17.46        16.57         8.42        30.81        21.34        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J 
        3.88        18.15        27.02        21.21        20.32        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       12.89        16.11        11.84         0.07        64.08         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM 
       51.78         1.22        45.37        13.74         4.21        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5D1 
       37.22        30.58        24.00        22.78        83.57        16.80 
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 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.13               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            174.08             154.32 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            21.070             18.165 
[1] "0.1 - 174.1 (21.1)" "0.0 - 154.3 (18.2)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         1       24       47        1        24        25
  19Q GAIN WILD-TYPE       1       63      104        1        39        67
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  19Q GAIN MUTATED           0         26          7        2
  19Q GAIN WILD-TYPE         3         36         14        5
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 24                 63
  STAGE IB                 47                104
  STAGE II                  1                  1
  STAGE IIA                24                 39
  STAGE IIB                25                 67
  STAGE III                 0                  3
  STAGE IIIA               26                 36
  STAGE IIIB                7                 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
  19Q GAIN MUTATED    30 100  18   9
  19Q GAIN WILD-TYPE  81 190  51  14
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               30                 81
  T2              100                190
  T3               18                 51
  T4                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                  N0  N1  N2  N3
  19Q GAIN MUTATED    96  45  16   0
  19Q GAIN WILD-TYPE 216  86  23   5
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               96                216
  N1               45                 86
  N2               16                 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   131   2
  19Q GAIN WILD-TYPE 273   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    131    2
  19Q GAIN WILD-TYPE  273    5
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0              131                273
  1                2                  5
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    40 117
  19Q GAIN WILD-TYPE  87 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     40  117
  19Q GAIN WILD-TYPE   87  249
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               40                 87
  MALE                117                249
[1] 2 2
[1] FALSE
D35V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                       8
  19Q GAIN WILD-TYPE                                     7
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                         1
  19Q GAIN WILD-TYPE                                       0
                    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                                                           148
  19Q GAIN WILD-TYPE                                                         322
D35V9, multiclass
                                                             clus
vv                                                            19Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      8
  LUNG CLEAR CELL 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)              148
                                                             clus
vv                                                            19Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                322
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3 154
  19Q GAIN WILD-TYPE  10 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3  154
  19Q GAIN WILD-TYPE   10  326
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 3                 10
  YES              154                326
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED   126   3   0   7
  19Q GAIN WILD-TYPE 268   9   4  15
D35V13, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0              126                268
  R1                3                  9
  R2                0                  4
  RX                7                 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       4                        12   105
  19Q GAIN WILD-TYPE     5                        19   235
D35V14, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN               12                 19
  WHITE                                  105                235
[1] 3 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  93
  19Q GAIN WILD-TYPE   5 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   93
  19Q GAIN WILD-TYPE    5  216
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               93                216
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   148 101
  20P GAIN WILD-TYPE 133  95
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               249                228 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               101                 95 
$`20P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        7.46        79.46         4.80       117.57        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-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 
      122.43         9.34       119.80        43.23        88.11        41.69 
TCGA-21-5786 TCGA-21-A5DI TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
       33.93        32.19         1.74        27.02        20.48        48.33 
TCGA-22-4595 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 
       24.13        13.12        32.02         9.57        31.73        64.93 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 
       44.25        71.34        11.74        18.84        30.12        56.32 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 
       22.06         7.63        98.01       103.53        54.44         1.55 
TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 
       27.02       110.99        44.19       118.36         2.63        61.61 
TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 
       28.96        32.88        65.23        23.24        12.00        18.15 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-4130 
        1.12         4.04        26.43        20.91         3.95         8.12 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 
        0.39         3.39        74.07        44.75        68.58         1.71 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 
       24.33        27.39        35.64        35.70        17.88        40.21 
TCGA-43-2578 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6773 TCGA-43-7656 
       22.49        33.11        27.91        12.36         3.81        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 
        7.76        66.51         2.93        11.61        12.03         9.99 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65        13.91         0.39        29.95        28.34         5.46 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 
        8.75        28.96        18.25         2.04         0.43         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8308 
        1.45         1.32         0.85         6.51        17.49        17.00 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZJ 
       16.77         1.81         1.18        20.94        19.23        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8391 TCGA-58-8393 
       18.74         0.13         2.76         0.03        71.24        34.78 
TCGA-58-A46K TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 
       34.36        21.11        10.22        96.82        37.94        21.93 
TCGA-60-2708 TCGA-60-2711 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       80.45        41.42        35.34        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML 
       35.90        11.77       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-66-2759 TCGA-66-2763 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 
        0.99        25.05         0.99         7.07        23.01         3.02 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2787 
        2.01        12.03         3.98        12.00        24.95        40.01 
TCGA-66-2788 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 TCGA-68-8250 
       22.98        30.02        10.06        49.05         6.64         8.02 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       13.35        16.18        29.56        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-8007 
       89.98        20.78         0.49        42.28         0.16         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8143 
       86.76        53.95        82.92        53.92        39.09        26.40 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        0.33       117.57        22.29        42.41        42.08        30.81 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 
       27.62        38.86         9.67        12.99        36.53        31.30 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 
        1.15        29.95        19.04        24.13        31.56        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8353 TCGA-85-8481 TCGA-85-8664 
       10.09         0.76        22.45         3.09         7.76         0.10 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M 
       15.62        19.33        17.72        14.96        18.18        12.56 
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-94-7557 TCGA-94-7943 TCGA-94-A5I4 
       22.62         3.48         5.26         0.16        11.70        16.14 
TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       17.69        57.07        19.36         2.76        30.81        30.67 
TCGA-98-A539 TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
        3.88         2.01        18.58        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HH 
       16.11        13.18        13.41         0.07         4.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HQ 
       45.37        13.74         4.21         2.89        24.00        14.73 
TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N 
       29.75        83.57         3.65        16.80         0.43        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52W 
        3.72        12.72         8.58 

$`20P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 
       12.20        75.75        92.15        31.99         1.64        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 
        6.18         2.79       154.32        27.19        99.16        70.16 
TCGA-21-1078 TCGA-21-1079 TCGA-21-5782 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
       15.58        31.73        31.63        10.82        21.99         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1017 TCGA-22-4593 
       14.93         4.31        64.21        14.10        48.82        35.08 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 
        0.56        38.17        34.75        19.30        11.77        63.55 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 
       14.63         0.79        54.28        79.20        62.86        16.64 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-6737 
      133.74        79.53       174.08       151.27        14.07        19.76 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASL TCGA-34-2604 
        4.70         0.30        36.62         6.94        27.16        31.50 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 
       31.27        67.79        56.38         9.07        16.93        30.94 
TCGA-34-5929 TCGA-34-8454 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
        4.96        27.19         0.43         0.39         6.58         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        7.82         6.81        47.80        55.20        70.03        60.79 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 
        1.94        36.39        15.58        17.06        38.66        27.02 
TCGA-43-5668 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-8116 
       18.38        24.89        21.47         5.46        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-51-4080 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 
        9.73        14.20         0.39        30.35        27.45         0.10 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        0.62         0.99         0.10         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
        1.35        22.75        10.36         9.93        20.25        15.81 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       13.32        17.85         0.26        13.25        13.55        29.95 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 
       16.47        85.12        56.65        35.24        29.92         3.58 
TCGA-60-2697 TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 
       12.23        92.71        49.48        66.54         9.01        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MH 
       50.33        48.49        32.32        23.57        26.83        66.61 
TCGA-63-A5MI TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MU 
       58.65        11.34        25.28        89.29        16.37        25.41 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       34.59        16.96        43.10         0.99         1.02         2.01 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
        0.92        43.99        21.01         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 
        2.01        19.00        19.00         1.97        25.97         4.04 
TCGA-66-2790 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-A59J TCGA-77-6843 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 
       14.73        73.12        70.13       106.95        46.78        15.75 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
       37.81        12.59        17.72       104.09        11.54        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ 
        6.97         9.63        54.41        65.49        35.90       126.18 
TCGA-77-A5G1 TCGA-77-A5G7 TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 
      132.36         5.92        11.97         6.41        34.95        32.91 
TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 
        1.38        18.94        25.15        14.07        16.87        13.22 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 
       16.77         5.29        32.71         2.01         0.72        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z 
       13.94        12.59        25.68        24.36        19.73        16.21 
TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A59Q 
       14.96         0.79        24.92         9.50        14.07        10.59 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 
        2.70         4.01         2.30        21.04         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       26.63        14.14        49.87        18.31        17.46        16.57 
TCGA-98-7454 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D 
        8.42        21.34        27.16        18.15        27.02        21.21 
TCGA-98-A53H TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HM TCGA-NC-A5HN 
       20.32        11.84        64.08        51.78        39.85        37.22 
TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CT TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       30.58        22.78        65.49        43.89        11.18         0.20 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.03               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            122.43             174.08 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            19.590             18.345 
[1] "0.0 - 122.4 (19.6)" "0.1 - 174.1 (18.3)"
[1] "hr=" "1"  
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         2       38       81        1        31        51
  20P GAIN WILD-TYPE       0       49       70        1        32        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  20P GAIN MUTATED           2         33          9        6
  20P GAIN WILD-TYPE         1         29         12        1
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 38                 49
  STAGE IB                 81                 70
  STAGE II                  1                  1
  STAGE IIA                31                 32
  STAGE IIB                51                 41
  STAGE III                 2                  1
  STAGE IIIA               33                 29
  STAGE IIIB                9                 12
  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    47 159  37  13
  20P GAIN WILD-TYPE  64 131  32  10
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               47                 64
  T2              159                131
  T3               37                 32
  T4               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                  N0  N1  N2  N3
  20P GAIN MUTATED   161  69  21   1
  20P GAIN WILD-TYPE 151  62  18   4
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              161                151
  N1               69                 62
  N2               21                 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   210   6
  20P GAIN WILD-TYPE 194   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    210    6
  20P GAIN WILD-TYPE  194    1
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              210                194
  1                6                  1
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    53 203
  20P GAIN WILD-TYPE  74 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     53  203
  20P GAIN WILD-TYPE   74  163
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               53                 74
  MALE                203                163
[1] 2 2
[1] FALSE
D36V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                      10
  20P GAIN WILD-TYPE                                     5
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                         1
  20P GAIN WILD-TYPE                                       0
                    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                                                           242
  20P GAIN WILD-TYPE                                                         228
D36V9, multiclass
                                                             clus
vv                                                            20P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              242
                                                             clus
vv                                                            20P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                228
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     9 247
  20P GAIN WILD-TYPE   4 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      9  247
  20P GAIN WILD-TYPE    4  233
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 9                  4
  YES              247                233
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, continuous
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED   203   6   3  12
  20P GAIN WILD-TYPE 191   6   1  10
D36V13, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              203                191
  R1                6                  6
  R2                3                  1
  RX               12                 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   177
  20P GAIN WILD-TYPE     3                        15   163
D36V14, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    6                  3
  BLACK OR AFRICAN AMERICAN               16                 15
  WHITE                                  177                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     7 158
  20P GAIN WILD-TYPE   1 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7  158
  20P GAIN WILD-TYPE    1  151
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                  1
  NOT HISPANIC OR LATINO              158                151
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   142  97
  20Q GAIN WILD-TYPE 139  99
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               239                238 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                97                 99 
$`20Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 
        7.46        79.46         4.80        11.34        23.54        36.07 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 
       49.94       119.54        46.88        60.89        34.78        31.73 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        9.34       119.80        43.23        41.69        33.93        10.82 
TCGA-21-A5DI TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       32.19         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4605 TCGA-22-5472 TCGA-22-5480 TCGA-22-5483 
       48.33        24.13        32.02        64.93        71.34        18.84 
TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 
       30.12        56.32        22.06         7.63        98.01       103.53 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 
       54.44         1.55        27.02       110.99        44.19         2.63 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 
       31.50        28.96        32.88        31.27        65.23        23.24 
TCGA-34-5240 TCGA-34-5928 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
       12.00        18.15         4.04        26.43        20.91         3.95 
TCGA-37-3792 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        0.39         8.12         6.81         0.39         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 
       74.07        44.75         1.71        24.33        27.39        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 TCGA-43-5670 
       35.70        17.88        40.21        22.49        33.11        27.91 
TCGA-43-6143 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56V 
       12.36         5.46        19.59        66.51         2.93        12.03 
TCGA-46-3768 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
        9.99        13.91         5.46        30.35         8.75        28.96 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       18.25         2.04         0.62         0.43         0.99         1.45 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8504 TCGA-56-8624 TCGA-56-8626 TCGA-56-A4BW 
        0.85        17.49        16.77         1.18         9.93        19.23 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8393 
       21.04        18.74         0.13         2.76         0.03        34.78 
TCGA-58-A46K TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       34.36        21.11        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2711 TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 
       80.45        41.42        50.33        35.34        42.64         3.19 
TCGA-60-2722 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML 
       29.85        11.77       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-66-2744 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2769 
        0.99         0.99        43.99        25.05         0.99         7.07 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 
       23.01         2.01        12.03         3.98        12.00         1.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 TCGA-68-8250 
       40.01        22.98        10.06        49.05         6.64         8.02 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 
       13.35        16.18        23.28        11.18        89.98        20.78 
TCGA-77-7141 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        0.49       106.95         0.16        46.78        15.75         6.51 
TCGA-77-8008 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8143 TCGA-77-8145 
       86.76        82.92        53.92        39.09        26.40         6.97 
TCGA-77-8148 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB 
        9.63       117.57        22.29         5.92        42.08        30.81 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 
       27.62        38.86         9.67        11.97        12.99        36.53 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 
        1.15        29.95        19.04        24.13        31.56        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-85-8481 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC 
        7.76        13.94         0.10        15.62        17.72        14.96 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 
       18.18        19.73        12.56        15.85        12.39         3.65 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 
        2.93        11.77        20.22        22.62         3.48         5.26 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 
        0.16        11.70        14.14        16.14        17.69        57.07 
TCGA-98-8020 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B TCGA-98-A53I 
        2.76        30.67        27.16         3.88         2.01        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        19.10        12.89        13.18        13.41        11.84 
TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
        0.07         4.54        51.78         1.22        45.37        13.74 
TCGA-NC-A5HM TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CX 
       39.85        24.00        14.73        29.75        83.57         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52W 
       16.80         0.43        33.07        12.72         8.58 

$`20Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 
       12.20        75.75       117.57        92.15        31.99         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 
       86.96         6.18         2.79       154.32        27.19        99.16 
TCGA-21-1075 TCGA-21-1078 TCGA-21-1080 TCGA-21-5782 TCGA-21-5783 TCGA-22-0940 
       70.16        15.58       122.43        31.63        88.11        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1017 TCGA-22-4596 
        7.33        14.93         4.31        64.21        48.82         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       38.17        34.75        13.12        19.30         9.57        11.77 
TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       31.73        63.55        14.63        44.25         0.79        54.28 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 TCGA-22-5492 TCGA-33-4533 TCGA-33-4547 
       79.20        11.74        62.86        16.64       133.74        79.53 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW 
      174.08       151.27        14.07        19.76         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-5232 
       36.62         6.94       118.36        27.16        61.61        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
       56.38         9.07        16.93        30.94         4.96         1.12 
TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-39-5021 
       27.19         0.43         6.58         7.46         7.82        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
       55.20        70.03        60.79         1.94        36.39        15.58 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-6647 TCGA-43-6770 
       17.06        38.66        27.02        18.38        24.89        21.47 
TCGA-43-6773 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 
        3.81         7.76        13.38        11.77        11.61         9.73 
TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       14.20        10.65         0.39         0.39        29.95        28.34 
TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
       27.45         0.10         0.99         1.32         6.51         0.10 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        3.48        26.89        17.00        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX 
       22.75        10.36        20.25        15.81        20.94        13.32 
TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
       17.85         0.26        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 
       16.47        85.12        56.65        35.24        29.92         3.58 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 
       12.23        10.22        49.48        66.54         9.01        56.91 
TCGA-60-2716 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MH 
       48.49        32.32        35.90        23.57        26.83        66.61 
TCGA-63-A5MI TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MU 
       58.65        11.34        25.28        89.29        16.37        25.41 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       34.59        16.96        43.10         1.02         2.01         0.92 
TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 
       21.01         2.01         1.02         2.01         2.01        19.00 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2783 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 
        3.02        19.00        24.95        25.97         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 
        5.03        30.02        54.08         4.01         2.73         6.94 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7142 TCGA-77-7335 
       14.73        29.56        73.12        75.09        42.28        70.13 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       53.95        37.81        12.59        17.72       104.09        11.54 
TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       27.39        54.41        65.49        35.90         0.33       126.18 
TCGA-77-A5G1 TCGA-77-A5G8 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
      132.36        42.41         6.41        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 
        1.38        18.94        25.15        14.07        16.87        13.22 
TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8584 TCGA-85-A4CL 
        5.29         2.01         0.72        14.63        12.59        25.68 
TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 
       19.33        24.36        16.21        14.96         0.79        24.92 
TCGA-90-7766 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 
        9.50        14.07        10.59         2.70         4.01         2.30 
TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-8169 
       21.04         4.01         5.03        26.63        49.87        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 
       17.46        19.36        16.57         8.42        30.81        21.34 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A524 TCGA-NC-A5HE 
       18.15        27.02        21.21        20.32        16.11        64.08 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CT 
        4.21         2.89        37.22        30.58        22.78        65.49 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        43.89        11.18         0.20 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.03               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            119.80             174.08 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             19.23              19.00 
[1] "0.0 - 119.8 (19.2)" "0.1 - 174.1 (19.0)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         2       38       77        0        31        45
  20Q GAIN WILD-TYPE       0       49       74        2        32        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  20Q GAIN MUTATED           1         33         10        6
  20Q GAIN WILD-TYPE         2         29         11        1
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 38                 49
  STAGE IB                 77                 74
  STAGE II                  0                  2
  STAGE IIA                31                 32
  STAGE IIB                45                 47
  STAGE III                 1                  2
  STAGE IIIA               33                 29
  STAGE IIIB               10                 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
  20Q GAIN MUTATED    48 148  35  14
  20Q GAIN WILD-TYPE  63 142  34   9
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               48                 63
  T2              148                142
  T3               35                 34
  T4               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                  N0  N1  N2  N3
  20Q GAIN MUTATED   155  66  20   0
  20Q GAIN WILD-TYPE 157  65  19   5
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              155                157
  N1               66                 65
  N2               20                 19
  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   202   6
  20Q GAIN WILD-TYPE 202   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    202    6
  20Q GAIN WILD-TYPE  202    1
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              202                202
  1                6                  1
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    47 198
  20Q GAIN WILD-TYPE  80 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     47  198
  20Q GAIN WILD-TYPE   80  168
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               47                 80
  MALE                198                168
[1] 2 2
[1] FALSE
D37V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                      11
  20Q GAIN WILD-TYPE                                     4
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                         1
  20Q GAIN WILD-TYPE                                       0
                    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                                                           230
  20Q GAIN WILD-TYPE                                                         240
D37V9, multiclass
                                                             clus
vv                                                            20Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              230
                                                             clus
vv                                                            20Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                240
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     8 237
  20Q GAIN WILD-TYPE   5 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8  237
  20Q GAIN WILD-TYPE    5  243
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 8                  5
  YES              237                243
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   194   5   1  12
  20Q GAIN WILD-TYPE 200   7   3  10
D37V13, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              194                200
  R1                5                  7
  R2                1                  3
  RX               12                 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
  20Q GAIN MUTATED       6                        16   168
  20Q GAIN WILD-TYPE     3                        15   172
D37V14, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    6                  3
  BLACK OR AFRICAN AMERICAN               16                 15
  WHITE                                  168                172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     6 155
  20Q GAIN WILD-TYPE   2 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6  155
  20Q GAIN WILD-TYPE    2  154
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO              155                154
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    34  20
  21Q GAIN WILD-TYPE 247 176
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                54                423 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                20                176 
$`21Q GAIN MUTATED`
TCGA-18-3410 TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-21-A5DI TCGA-22-1011 
        4.80        34.78         9.34       119.80        32.19         1.74 
TCGA-22-4595 TCGA-22-A5C4 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-34-2596 
       24.13        22.06       174.08       151.27        54.44         2.63 
TCGA-34-2605 TCGA-34-5240 TCGA-34-5928 TCGA-39-5028 TCGA-43-6143 TCGA-43-6647 
       28.96        12.00        18.15         1.71        12.36        24.89 
TCGA-43-A475 TCGA-56-7221 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2706 
        9.73         0.99        17.00        16.77        17.85        92.71 
TCGA-60-2714 TCGA-60-2724 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MR TCGA-66-2756 
       50.33        23.57        70.62        66.61        89.29         0.99 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2783 TCGA-77-6844 TCGA-77-7139 TCGA-77-8130 
        2.01        23.01        24.95        75.09        89.98        82.92 
TCGA-77-8139 TCGA-77-8143 TCGA-77-A5G7 TCGA-77-A5GA TCGA-85-6560 TCGA-85-7844 
      104.09        26.40         5.92        42.08        11.97        29.95 
TCGA-85-7950 TCGA-85-8277 TCGA-85-8353 TCGA-85-A4JB TCGA-92-7340 TCGA-96-7545 
       18.94        10.09         3.09        17.72         2.70        57.07 
TCGA-LA-A7SW TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HR TCGA-NC-A5HT TCGA-O2-A5IB 
       13.41        51.78        45.37        29.75        22.78        11.18 

$`21Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       23.54        92.15        31.99        36.07         1.64        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
        6.18         2.79       154.32        49.94        27.19       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
       46.88        99.16        70.16        60.89        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-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       10.82        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
       14.10        27.02        48.82        20.48        35.08        48.33 
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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
        9.57        11.77        31.73        64.93        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        54.28        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 
       18.84        30.12        62.86        56.32        16.64         7.63 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 
      133.74        98.01        79.53       103.53        14.07         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       19.76        27.02         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 
      110.99        44.19       118.36        27.16        61.61        31.50 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       32.88        31.27        65.23        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       23.24        16.93        30.94         4.96         1.12        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
        4.04        26.43        20.91         3.95         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        6.58         8.12         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        3.39        47.80        74.07        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       70.03        60.79        24.33         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
       15.58        35.64        35.70        17.88        17.06        40.21 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       22.49        38.66        27.02        33.11        18.38        27.91 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
       21.47         5.46         3.81        19.59         7.76        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
       13.38        11.77         2.93        11.61        14.20        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.99        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-56-1622 
       28.34         5.46        30.35         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 
        0.10        18.25         2.04         0.62         0.43         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
        1.45         1.32         0.85         6.51         0.10        17.49 
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 
        1.18        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
       19.23        13.32        21.04        18.74         0.13         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        2.76         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-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       29.92        21.11         3.58        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       37.94        21.93        80.45        49.48        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
        9.01        56.91        35.34        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       32.32        29.85        35.90        26.83        11.77       102.67 
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-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       78.28        16.37        25.41        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-66-2757 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-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
        2.01         1.02         2.01         7.07        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 
        2.01        19.00        12.03         3.98        12.00         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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        6.64         6.94         8.02        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 
       29.56        73.12        23.28        11.18        20.78         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       42.28        70.13       106.95         0.16        46.78        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
        6.51        86.76        53.95        37.81        12.59        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       39.09        17.72        11.54        27.39         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       54.41        65.49        35.90         0.33       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
      117.57        22.29        42.41        30.81        27.62        38.86 
TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
        9.67        12.99         6.41        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
       32.91         1.38         1.15        25.15        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
       31.56        14.07        16.87        34.52         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       22.45        16.77         5.29        32.71         2.01         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        7.76        14.63        13.94        12.59         0.10        15.62 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       25.68        19.33        14.96        24.36        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       12.56        16.21        15.85        14.96         0.79        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
        3.65        24.92         9.50         2.93        11.77        14.07 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       20.22        22.62        10.59         3.48         4.01         5.26 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.30        21.04         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
       26.63        14.14        16.14        17.69        49.87        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 
       17.46        19.36        16.57         8.42         2.76        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
       30.67        21.34        27.16         3.88        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       27.02        21.21        20.32        18.58        20.71        19.10 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       12.89        16.11        13.18        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
        4.54         1.22        13.74         4.21         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CT 
       37.22        30.58        24.00        14.73        83.57        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
        3.65        16.80         0.43        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       43.89         8.58         0.20 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.99               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            174.08             154.32 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             23.29              19.00 
[1] "1.0 - 174.1 (23.3)" "0.0 - 154.3 (19.0)"
[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       15        0         4        13
  21Q GAIN WILD-TYPE       2       81      136        2        59        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  21Q GAIN MUTATED           1         12          4        0
  21Q GAIN WILD-TYPE         2         50         17        7
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  6                 81
  STAGE IB                 15                136
  STAGE II                  0                  2
  STAGE IIA                 4                 59
  STAGE IIB                13                 79
  STAGE III                 1                  2
  STAGE IIIA               12                 50
  STAGE IIIB                4                 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
  21Q GAIN MUTATED     7  32  14   3
  21Q GAIN WILD-TYPE 104 258  55  20
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                7                104
  T2               32                258
  T3               14                 55
  T4                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                  N0  N1  N2  N3
  21Q GAIN MUTATED    29  22   3   2
  21Q GAIN WILD-TYPE 283 109  36   3
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               29                283
  N1               22                109
  N2                3                 36
  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    45   0
  21Q GAIN WILD-TYPE 359   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     45    0
  21Q GAIN WILD-TYPE  359    7
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               45                359
  1                0                  7
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    11  45
  21Q GAIN WILD-TYPE 116 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     11   45
  21Q GAIN WILD-TYPE  116  321
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               11                116
  MALE                 45                321
[1] 2 2
[1] FALSE
D38V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                       4
  21Q GAIN WILD-TYPE                                    11
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                         0
  21Q GAIN WILD-TYPE                                       1
                    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                                                            51
  21Q GAIN WILD-TYPE                                                         419
D38V9, multiclass
                                                             clus
vv                                                            21Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               51
                                                             clus
vv                                                            21Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                419
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3  53
  21Q GAIN WILD-TYPE  10 427
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3   53
  21Q GAIN WILD-TYPE   10  427
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 3                 10
  YES               53                427
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    41   3   1   5
  21Q GAIN WILD-TYPE 353   9   3  17
D38V13, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               41                353
  R1                3                  9
  R2                1                  3
  RX                5                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       1                         1    40
  21Q GAIN WILD-TYPE     8                        30   300
D38V14, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                1                 30
  WHITE                                   40                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"
D38V15, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  34
  21Q GAIN WILD-TYPE   8 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   34
  21Q GAIN WILD-TYPE    8  275
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               34                275
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED   132  78
  22Q GAIN WILD-TYPE 149 118
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               210                267 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                78                118 
$`22Q GAIN MUTATED`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-21-1072 
       75.75        79.46       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-33-4532 
       54.28        79.20        11.74        56.32        16.64         7.63 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 
       14.07         1.55        27.02       110.99       118.36         2.63 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5236 
       61.61        28.96        32.88        31.27        65.23         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       23.24        12.00        16.93         4.04        26.43        20.91 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4141 TCGA-39-5019 TCGA-39-5021 TCGA-39-5034 
        8.12         7.82         0.39        44.75        68.58        36.39 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       35.64        35.70        17.88        27.02        33.11        18.38 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 
       27.91        24.89        21.47         7.76         2.93        11.61 
TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 
        9.73        12.03         9.99        10.65         5.46        30.35 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 
        8.75        28.96         0.10        18.25         2.04         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
        1.45         1.32         0.85         6.51         0.10        17.49 
TCGA-56-8308 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8626 TCGA-56-8629 
       17.00         1.35        16.77         1.81         9.93        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
       20.94        19.23        13.32        21.04         0.13         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 
        0.03        13.25        29.95        35.24        29.92        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2714 
       37.94        92.71        21.93        80.45        41.42        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
       42.64         3.19        29.85        35.90        26.83        11.77 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MS 
      102.67        70.62        66.61        58.65        45.57        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       16.37        36.16        53.88        43.10         2.01        21.07 
TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 
        0.92        21.01         0.99         7.07         3.02         2.01 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2792 TCGA-66-2794 
        3.98        24.95         1.97        22.98        30.02        54.08 
TCGA-66-2800 TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 
       49.05        14.73        29.56        23.28        89.98        20.78 
TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
        0.49         0.16        46.78         6.51        86.76        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 
       82.92        12.59        53.92        11.54        26.40         6.97 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB 
       65.49         0.33       132.36         5.92        42.08        30.81 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 
       27.62        38.86         9.67        12.99        36.53        31.30 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8354 
       24.13        31.56        34.52        10.09        22.45        32.71 
TCGA-85-8481 TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ 
        7.76        14.63        19.33        17.72        14.96        18.18 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-92-7341 
       19.73        12.56         3.65         2.93        11.77         3.48 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 
       21.04        11.70        14.14        16.14        17.69        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8022 TCGA-98-A538 
       18.31        17.46        19.36         2.76        30.67        27.16 
TCGA-98-A539 TCGA-98-A53J TCGA-J1-A4AH TCGA-LA-A446 TCGA-NC-A5HD TCGA-NC-A5HG 
        3.88        20.71        19.10        13.18         0.07        51.78 
TCGA-NC-A5HI TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NK-A5CR TCGA-O2-A52N TCGA-XC-AA0X 
       45.37        37.22        24.00        83.57        33.07         0.20 

$`22Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
       12.20         7.46         4.80        92.15        31.99        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
        1.64        86.96         6.18         2.79       154.32        49.94 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
       27.19       119.54        46.88        15.58       122.43         9.34 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
       31.63        88.11        10.82        32.19        21.99         7.33 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 
       14.93        64.21        27.02        48.82        48.33         0.56 
TCGA-22-4599 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       38.17        19.30         9.57        11.77        31.73        64.93 
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-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        22.06       133.74        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW 
      103.53       151.27        54.44        19.76         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2604 TCGA-34-5232 
       36.62         6.94        44.19        27.16        31.50        67.79 
TCGA-34-5234 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       56.38        30.94        18.15         4.96         1.12        27.19 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 
        3.95         0.43         0.39         6.58         7.46         6.81 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        3.39        47.80        74.07        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5040 
        1.71        24.33         1.94        27.39        15.58        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-6143 TCGA-43-6771 TCGA-43-6773 
       40.21        22.49        38.66        12.36         5.46         3.81 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-6026 
       19.59        66.51        13.38        11.77        14.20        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 TCGA-56-6546 
        0.39         0.39        29.95        28.34        27.45         0.62 
TCGA-56-7222 TCGA-56-7223 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8623 
        0.43         0.99         3.48        26.89        14.07        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T 
        1.18        10.36        20.25        17.85        18.74         2.76 
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-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2709 
       56.65        21.11         3.58        12.23        10.22        49.48 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 
       66.54         9.01        56.91        35.34        48.49        32.32 
TCGA-60-2724 TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       23.57        59.97        14.99        11.34        25.28        89.29 
TCGA-63-A5MU TCGA-63-A5MY TCGA-66-2727 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       25.41        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-68-8250 TCGA-68-8251 
        4.01         2.73         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 
       16.18        73.12        75.09        11.18        42.28        70.13 
TCGA-77-7337 TCGA-77-7465 TCGA-77-8009 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
      106.95        15.75        53.95        39.09        17.72       104.09 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 
       27.39         9.63        54.41        35.90       126.18       117.57 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 
       22.29        42.41        11.97         6.41        34.95        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-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
       14.07        16.87         0.76        13.22        16.77         5.29 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        3.09         2.01         0.72        13.94        12.59         0.10 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       15.62        25.68        24.36        16.21        15.85        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED 
        0.79        12.39        24.92         9.50        14.07        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-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-A4JL 
        0.16         4.01         5.03        26.63        49.87        16.57 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
        8.42        30.81        21.34        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW 
       21.21        20.32        18.58        12.89        16.11        13.41 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
       11.84        64.08         4.54         1.22        13.74         4.21 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT 
        2.89        39.85        30.58        14.73        29.75        22.78 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52S 
       65.49         3.65        16.80         0.43         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       43.89         8.58        11.18 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.03               0.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            132.36             174.08 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            21.025             17.720 
[1] "0.0 - 132.4 (21.0)" "0.1 - 174.1 (17.7)"
[1] "hr=" "1.2"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         1       31       77        0        27        45
  22Q GAIN WILD-TYPE       1       56       74        2        36        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  22Q GAIN MUTATED           0         20          8        5
  22Q GAIN WILD-TYPE         3         42         13        2
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 31                 56
  STAGE IB                 77                 74
  STAGE II                  0                  2
  STAGE IIA                27                 36
  STAGE IIB                45                 47
  STAGE III                 0                  3
  STAGE IIIA               20                 42
  STAGE IIIB                8                 13
  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    41 139  26  10
  22Q GAIN WILD-TYPE  70 151  43  13
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               41                 70
  T2              139                151
  T3               26                 43
  T4               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                  N0  N1  N2  N3
  22Q GAIN MUTATED   145  51  14   1
  22Q GAIN WILD-TYPE 167  80  25   4
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0              145                167
  N1               51                 80
  N2               14                 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   181   5
  22Q GAIN WILD-TYPE 223   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED    181    5
  22Q GAIN WILD-TYPE  223    2
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0              181                223
  1                5                  2
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    48 168
  22Q GAIN WILD-TYPE  79 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     48  168
  22Q GAIN WILD-TYPE   79  198
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               48                 79
  MALE                168                198
[1] 2 2
[1] FALSE
D39V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                       5
  22Q GAIN WILD-TYPE                                    10
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                         1
  22Q GAIN WILD-TYPE                                       0
                    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                                                           209
  22Q GAIN WILD-TYPE                                                         261
D39V9, multiclass
                                                             clus
vv                                                            22Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              209
                                                             clus
vv                                                            22Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                261
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     5 211
  22Q GAIN WILD-TYPE   8 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5  211
  22Q GAIN WILD-TYPE    8  269
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 5                  8
  YES              211                269
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED   179   6   1   5
  22Q GAIN WILD-TYPE 215   6   3  17
D39V13, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0              179                215
  R1                6                  6
  R2                1                  3
  RX                5                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       2                         9   151
  22Q GAIN WILD-TYPE     7                        22   189
D39V14, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                9                 22
  WHITE                                  151                189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3 133
  22Q GAIN WILD-TYPE   5 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3  133
  22Q GAIN WILD-TYPE    5  176
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO              133                176
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    43  22
  XP GAIN WILD-TYPE 238 174
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               65               412 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               22               174 
$`XP GAIN MUTATED`
TCGA-18-3406 TCGA-18-3421 TCGA-18-4083 TCGA-21-1081 TCGA-21-5786 TCGA-22-4593 
       12.20        86.96         6.18         9.34        33.93        35.08 
TCGA-22-4595 TCGA-33-4532 TCGA-33-4587 TCGA-33-A4WN TCGA-33-AASI TCGA-34-2596 
       24.13         7.63        54.44         4.70        44.19         2.63 
TCGA-34-5240 TCGA-34-5928 TCGA-37-5819 TCGA-39-5019 TCGA-39-5036 TCGA-43-3920 
       12.00        18.15         3.39        44.75        35.64        33.11 
TCGA-43-5670 TCGA-43-7657 TCGA-43-7658 TCGA-43-A475 TCGA-56-7223 TCGA-56-7730 
       27.91         7.76        66.51         9.73         0.99         6.51 
TCGA-56-8307 TCGA-56-8504 TCGA-56-A4BW TCGA-58-8386 TCGA-58-A46M TCGA-58-A46N 
       26.89        16.77        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-A5MU TCGA-63-A5MW TCGA-66-2756 TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 
       25.41        53.88         0.99        21.01         1.02         7.07 
TCGA-66-2793 TCGA-77-7138 TCGA-77-7140 TCGA-77-7335 TCGA-77-8136 TCGA-77-8153 
       10.06        11.18        20.78        70.13        39.09        65.49 
TCGA-77-8156 TCGA-85-7710 TCGA-85-8070 TCGA-85-8072 TCGA-85-8350 TCGA-92-7341 
        0.33         1.38        31.56        16.87        22.45         3.48 
TCGA-94-7557 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8022 TCGA-98-A538 
        0.16        14.14        16.14        19.36        30.67        27.16 
TCGA-J1-A4AH TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NK-A7XE 
       19.10         1.22         4.21        37.22         0.43 

$`XP GAIN WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
        7.46        75.75        79.46         4.80       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 
       23.54        92.15        31.99        36.07         1.64         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
      154.32        49.94        27.19       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-21-1082 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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       32.19        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 
        1.74        14.10        27.02        48.82        20.48        48.33 
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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
        9.57        11.77        31.73        64.93        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        54.28        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       18.84        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
      133.74        98.01        79.53       174.08       103.53       151.27 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AAS8 
       14.07         1.55        19.76        27.02         0.30        36.62 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 
        6.94       110.99       118.36        27.16        61.61        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       28.96        32.88        31.27        65.23        67.79        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
        9.07        23.24        16.93        30.94         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       27.19         4.04        26.43        20.91         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.39         6.58         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        0.39        47.80        74.07        68.58        55.20        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       60.79         1.71        24.33         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
       15.58        35.70        17.88        17.06        40.21        22.49 
TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       38.66        27.02        18.38        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        5.46         3.81        19.59        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       11.61        14.20        12.03         9.99        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-56-5898 TCGA-56-6545 
        8.75        27.45        28.96         0.10        18.25         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
        0.62         0.99         0.43         1.45         1.32         0.85 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 
        0.10        17.49         3.48        17.00        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         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       15.81        20.94        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.13         0.26         2.76        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-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
        3.58        12.23        10.22        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
       80.45        49.48        66.54        41.42         9.01        56.91 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
       50.33        35.34        48.49         3.19        32.32        29.85 
TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       35.90        26.83       102.67        70.62        66.61        58.65 
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-66-2734 TCGA-66-2737 
       16.37        36.16        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-66-2773 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-66-2794 TCGA-66-2795 
        4.04        22.98         5.03        30.02        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       49.05         2.73         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       16.18        14.73        29.56        73.12        75.09        23.28 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
       89.98         0.49        42.28       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       15.75         6.51        86.76        53.95        37.81        82.92 
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-77-8154 TCGA-77-A5FZ 
       27.39         6.97         9.63        54.41        35.90       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
      132.36       117.57        22.29         5.92        42.41        42.08 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       30.81        27.62        38.86         9.67        11.97        12.99 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 
        6.41        36.53        34.95        31.30        32.91         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        14.07 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
       34.52        10.09         0.76        13.22        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         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       13.94        12.59         0.10        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       17.72        14.96        24.36        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96         0.79        12.39         3.65 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
       24.92         9.50         2.93        11.77        14.07        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-94-7033 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 
       21.04        11.70         4.01         5.03        26.63        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       49.87        57.07        18.31        17.46        16.57         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
        2.76        30.81        21.34         3.88        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       27.02        21.21        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       16.11        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HM 
        4.54        51.78        45.37        13.74         2.89        39.85 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       30.58        24.00        14.73        29.75        22.78        83.57 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       65.49         3.65        16.80        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89         8.58        11.18         0.20 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.03              0.07 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            96.82            174.08 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            19.23             19.02 
[1] "0.0 - 96.8 (19.2)"  "0.1 - 174.1 (19.0)"
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         0        9       21        0         9        15
  XP GAIN WILD-TYPE       2       78      130        2        54        77
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  XP GAIN MUTATED           0          5          5        1
  XP GAIN WILD-TYPE         3         57         16        6
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 9                78
  STAGE IB                21               130
  STAGE II                 0                 2
  STAGE IIA                9                54
  STAGE IIB               15                77
  STAGE III                0                 3
  STAGE IIIA               5                57
  STAGE IIIB               5                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
  XP GAIN MUTATED    10  42   8   5
  XP GAIN WILD-TYPE 101 248  61  18
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              10               101
  T2              42               248
  T3               8                61
  T4               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                 N0  N1  N2  N3
  XP GAIN MUTATED    40  19   5   0
  XP GAIN WILD-TYPE 272 112  34   5
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              40               272
  N1              19               112
  N2               5                34
  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    54   1
  XP GAIN WILD-TYPE 350   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     54    1
  XP GAIN WILD-TYPE  350    6
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              54               350
  1               1                 6
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    17  48
  XP GAIN WILD-TYPE 110 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     17   48
  XP GAIN WILD-TYPE  110  318
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              17               110
  MALE                48               318
[1] 2 2
[1] FALSE
D40V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  XP GAIN MUTATED                                       4
  XP GAIN WILD-TYPE                                    11
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  XP GAIN MUTATED                                         0
  XP GAIN WILD-TYPE                                       1
                   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                                                            60
  XP GAIN WILD-TYPE                                                         410
D40V9, multiclass
                                                             clus
vv                                                            XP GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              60
                                                             clus
vv                                                            XP GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               410
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     1  64
  XP GAIN WILD-TYPE  12 416
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1   64
  XP GAIN WILD-TYPE   12  416
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                1                12
  YES              64               416
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, continuous
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    51   3   0   2
  XP GAIN WILD-TYPE 343   9   4  20
D40V13, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              51               343
  R1               3                 9
  R2               0                 4
  RX               2                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         3    49
  XP GAIN WILD-TYPE     9                        28   291
D40V14, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               3                28
  WHITE                                  49               291
[1] 3 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   8 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   43
  XP GAIN WILD-TYPE    8  266
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              43               266
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    53  28
  XQ GAIN WILD-TYPE 228 168
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               81               396 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               168 
$`XQ GAIN MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 
       12.20         7.46        75.75        11.34        36.07        86.96 
TCGA-18-4083 TCGA-21-1081 TCGA-21-5786 TCGA-22-1012 TCGA-22-4593 TCGA-22-4595 
        6.18         9.34        33.93        14.10        35.08        24.13 
TCGA-22-5483 TCGA-33-4532 TCGA-33-4566 TCGA-33-AASJ TCGA-34-2596 TCGA-34-5240 
       18.84         7.63       174.08       118.36         2.63        12.00 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-34-8456 TCGA-37-4133 TCGA-37-5819 
       30.94        18.15        27.19        26.43         7.82         3.39 
TCGA-39-5019 TCGA-43-3920 TCGA-43-5670 TCGA-43-7657 TCGA-43-A475 TCGA-51-4079 
       44.75        33.11        27.91         7.76         9.73         0.39 
TCGA-56-7223 TCGA-56-7730 TCGA-56-8504 TCGA-56-8624 TCGA-56-8629 TCGA-56-A4BW 
        0.99         6.51        16.77         1.18        15.81        19.23 
TCGA-58-8386 TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2703 TCGA-60-2711 
        0.03        35.24        29.92        21.11        96.82        41.42 
TCGA-60-2719 TCGA-60-2724 TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MU 
       42.64        23.57        45.57        25.28        16.37        25.41 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 TCGA-66-2781 
        0.99        21.01         1.02         7.07         3.02         3.98 
TCGA-66-2792 TCGA-66-2793 TCGA-77-6842 TCGA-77-7138 TCGA-77-7140 TCGA-77-7335 
       30.02        10.06        29.56        11.18        20.78        70.13 
TCGA-77-8009 TCGA-77-8156 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-7710 
       53.95         0.33        42.08        27.62        12.99         1.38 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8350 TCGA-85-8354 TCGA-85-A50M TCGA-92-7341 
       31.56        16.87        22.45        32.71        12.56         3.48 
TCGA-94-7557 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-A538 
        0.16        14.14        16.14        17.69        19.36        27.16 
TCGA-J1-A4AH TCGA-NC-A5HN TCGA-NK-A7XE 
       19.10        37.22         0.43 

$`XQ GAIN WILD-TYPE`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
       79.46         4.80       117.57        23.54        92.15        31.99 
TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
        1.64         2.79       154.32        49.94        27.19       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-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       41.69        10.82        32.19        21.99         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        4.31        64.21         1.74        27.02        48.82        20.48 
TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       48.33         0.56        38.17        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        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        54.28        71.34        79.20 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       11.74        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
      133.74        98.01        79.53       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       54.44         1.55        19.76        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 
       36.62         6.94       110.99        44.19        27.16        61.61 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
       31.50        28.96        32.88        31.27        65.23        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5929 TCGA-34-7107 
       56.38         9.07        23.24        16.93         4.96         1.12 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
        4.04        20.91         3.95         0.43         0.39         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 
        8.12         7.46         6.81         0.39        47.80        74.07 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        70.03        60.79         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        27.39        36.39        15.58        35.64        35.70 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
       17.88        17.06        40.21        22.49        38.66        27.02 
TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       18.38        12.36        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
       19.59        66.51        13.38        11.77         2.93        11.61 
TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 
       14.20        12.03         9.99        10.65        13.91         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
       29.95        28.34         5.46        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
       28.96         0.10        18.25         2.04         0.62         0.99 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
        0.43         1.45         1.32         0.85         0.10        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        3.48        26.89        17.00        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX 
       22.75        10.36         9.93        20.25        20.94        13.32 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T 
       17.85        21.04        18.74         0.13         0.26         2.76 
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-60-2696 TCGA-60-2697 TCGA-60-2698 
       85.12        34.36        56.65         3.58        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-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
        9.01        56.91        50.33        35.34        48.49         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       32.32        29.85        35.90        26.83        11.77       102.67 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN 
       70.62        66.61        58.65        59.97        14.99        11.34 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       89.29        78.28        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-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
        0.92        43.99        25.05         0.99         2.01         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        2.01        23.01        19.00         2.01        19.00        12.03 
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-66-2794 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-68-8250 TCGA-68-8251 TCGA-68-A59I 
        2.73         6.64         6.94         8.02        13.35        16.18 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
       14.73        73.12        75.09        23.28        89.98         0.49 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       42.28       106.95         0.16        46.78        15.75         6.51 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       86.76        37.81        82.92        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-A5FZ TCGA-77-A5G1 
        9.63        54.41        65.49        35.90       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH 
      117.57        22.29         5.92        42.41        30.81        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
        9.67        11.97         6.41        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       32.91         1.15        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       24.13        14.07        34.52        10.09         0.76        13.22 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         5.29         3.09         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       19.33        17.72        14.96        24.36        18.18        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         0.79        12.39         3.65 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
       24.92         9.50         2.93        11.77        14.07        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-94-7033 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 
       21.04        11.70         4.01         5.03        26.63        49.87 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       57.07        18.31        17.46        16.57         8.42         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
       30.81        30.67        21.34         3.88        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       27.02        21.21        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       16.11        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        51.78         1.22        45.37        13.74         4.21 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR 
        2.89        39.85        30.58        24.00        14.73        29.75 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N 
       22.78        83.57        65.49         3.65        16.80        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        12.72        43.89         8.58        11.18         0.20 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.03              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           174.08            154.32 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           18.840            19.315 
[1] "0.0 - 174.1 (18.8)" "0.1 - 154.3 (19.3)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         0        7       29        0        14        18
  XQ GAIN WILD-TYPE       2       80      122        2        49        74
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  XQ GAIN MUTATED           0          6          6        2
  XQ GAIN WILD-TYPE         3         56         15        5
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 7                80
  STAGE IB                29               122
  STAGE II                 0                 2
  STAGE IIA               14                49
  STAGE IIB               18                74
  STAGE III                0                 3
  STAGE IIIA               6                56
  STAGE IIIB               6                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
  XQ GAIN MUTATED     9  56  11   6
  XQ GAIN WILD-TYPE 102 234  58  17
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               9               102
  T2              56               234
  T3              11                58
  T4               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                 N0  N1  N2  N3
  XQ GAIN MUTATED    50  25   5   0
  XQ GAIN WILD-TYPE 262 106  34   5
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              50               262
  N1              25               106
  N2               5                34
  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    69   2
  XQ GAIN WILD-TYPE 335   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     69    2
  XQ GAIN WILD-TYPE  335    5
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              69               335
  1               2                 5
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    17  65
  XQ GAIN WILD-TYPE 110 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     17   65
  XQ GAIN WILD-TYPE  110  301
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              17               110
  MALE                65               301
[1] 2 2
[1] FALSE
D41V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED                                       3
  XQ GAIN WILD-TYPE                                    12
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED                                         0
  XQ GAIN WILD-TYPE                                       1
                   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                                                            78
  XQ GAIN WILD-TYPE                                                         392
D41V9, multiclass
                                                             clus
vv                                                            XQ GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG CLEAR CELL 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)              78
                                                             clus
vv                                                            XQ GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               392
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     2  80
  XQ GAIN WILD-TYPE  11 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   80
  XQ GAIN WILD-TYPE   11  400
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                2                11
  YES              80               400
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    67   3   0   3
  XQ GAIN WILD-TYPE 327   9   4  19
D41V13, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              67               327
  R1               3                 9
  R2               0                 4
  RX               3                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    56
  XQ GAIN WILD-TYPE     6                        27   284
D41V14, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               4                27
  WHITE                                  56               284
[1] 3 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  55
  XQ GAIN WILD-TYPE   8 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   55
  XQ GAIN WILD-TYPE    8  254
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              55               254
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    82  61
  1P LOSS WILD-TYPE 199 135
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              143               334 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               61               135 
$`1P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3415 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 
       12.20        75.75        92.15        49.94        46.88        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1017 
       70.16        34.78        33.93        21.99         7.33        48.82 
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-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-33-4538 
       31.73        63.55        14.63        44.25        54.28        98.01 
TCGA-33-4583 TCGA-33-4586 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI 
      151.27        14.07         0.30        36.62         6.94        44.19 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-8456 TCGA-37-4129 
       27.16         2.63        61.61        28.96        26.43         6.58 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5027 TCGA-39-5029 TCGA-39-5034 TCGA-43-2581 
        3.39        74.07        60.79        24.33        36.39        38.66 
TCGA-43-3394 TCGA-43-7657 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 
       27.02         7.76        11.61        12.03         9.99        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-56-1622 
        0.39         0.39        29.95        28.34         8.75        28.96 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7822 
       18.25         2.04         0.99         1.32         6.51        17.49 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A62T TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L 
       20.94        13.32         2.76        16.47        34.78        56.65 
TCGA-58-A46M TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2714 TCGA-63-A5MB 
       35.24        10.22        92.71        21.93        50.33       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-77-7139 TCGA-77-7337 TCGA-77-7465 
        2.73         6.94        14.73        89.98       106.95        15.75 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G3 
       53.95        37.81        53.92         9.63        54.41       117.57 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 
       27.62         9.67        12.99        36.53        31.30         1.15 
TCGA-85-8049 TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8580 
       19.04        10.09         0.76         5.29         3.09        14.63 
TCGA-85-A4CN TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-A4EE TCGA-92-7341 
       19.33        14.96        12.39         3.65        22.62         3.48 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 
       11.70        16.14        49.87        57.07        19.36        30.81 
TCGA-98-8023 TCGA-98-A539 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 
       21.34         3.88        18.58        20.71        16.11        13.18 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       11.84        64.08         2.89        30.58        24.00        14.73 
TCGA-NC-A5HR TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V 
       29.75        83.57        33.07        12.72        43.89 

$`1P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        7.46        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       31.99        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
      154.32        27.19       119.54        60.89        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-21-A5DI TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       41.69        10.82        32.19        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4601 
        1.74        14.10        27.02        20.48        48.33        34.75 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5478 TCGA-22-5480 
       32.02        19.30        11.77        64.93         0.79        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-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 
       16.64        22.06         7.63       133.74        79.53       174.08 
TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
      103.53        54.44         1.55        19.76        27.02         4.70 
TCGA-33-AASD TCGA-33-AASJ TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
      110.99       118.36        31.50        32.88        31.27        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       67.79        56.38         9.07        23.24        12.00        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       30.94        18.15         4.96         1.12        27.19         4.04 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 
       20.91         3.95         0.43         0.39         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
        7.82         6.81         0.39        47.80        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 
       55.20        70.03         1.71         1.94        27.39        15.58 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
       35.64        35.70        17.88        17.06        40.21        22.49 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       33.11        18.38        27.91        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        5.46         3.81        19.59        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 
        2.93         9.73        14.20        10.65         5.46        30.35 
TCGA-52-7812 TCGA-56-5897 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
       27.45         0.10         0.62         0.99         0.43         1.45 
TCGA-56-7582 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.85         0.10         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
        9.93        20.25        15.81        19.23        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.13         0.26         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N TCGA-60-2695 
       29.95        71.24        85.12        34.36        29.92        21.11 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 
        3.58        12.23        96.82        37.94        80.45        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
       66.54        41.42         9.01        56.91        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       42.64         3.19        32.32        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM 
       26.83        11.77        70.62        66.61        58.65        14.99 
TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       11.34        78.28        16.37        25.41        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-66-2759 TCGA-66-2763 
        2.01         0.92         0.99        43.99        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 
        2.01         1.02         2.01         7.07        19.00        19.00 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 
       12.03        12.00        24.95         1.97        25.97        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
        4.04        22.98         6.64         8.02        13.35        16.18 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 
       29.56        73.12        75.09        23.28        11.18        20.78 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
        0.49        42.28        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        82.92        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        35.90 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        0.33       126.18       132.36        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 
       42.08        30.81        38.86        11.97         6.41        34.95 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 
       32.91         1.38        29.95        18.94        25.15        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8288 TCGA-85-8350 
       31.56        14.07        16.87        34.52        13.22        22.45 
TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 
       16.77        32.71         2.01         0.72         7.76        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC 
       12.59         0.10        15.62        25.68        17.72        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        18.18        19.73        12.56        16.21        15.85 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
        0.79        24.92         9.50         2.93        11.77        14.07 
TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       20.22        10.59         2.70         4.01         5.26         2.30 
TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
       21.04         0.16         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       17.69        18.31        17.46        16.57         8.42         2.76 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       30.67        27.16        18.15         2.01        27.02        21.21 
TCGA-98-A53H TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF 
       20.32        19.10        12.89        13.41         0.07         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM 
       51.78         1.22        45.37        13.74         4.21        39.85 
TCGA-NC-A5HN TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE 
       37.22        22.78        65.49         3.65        16.80         0.43 
TCGA-O2-A52Q TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72         8.58        11.18         0.20 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.30              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           151.27            174.08 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            21.34             18.56 
[1] "0.3 - 151.3 (21.3)" "0.0 - 174.1 (18.6)"
[1] "hr=" "1"  
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         1       22       41        1        24        27
  1P LOSS WILD-TYPE       1       65      110        1        39        65
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  1P LOSS MUTATED           1         21          8        1
  1P LOSS WILD-TYPE         2         41         13        6
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                22                65
  STAGE IB                41               110
  STAGE II                 1                 1
  STAGE IIA               24                39
  STAGE IIB               27                65
  STAGE III                1                 2
  STAGE IIIA              21                41
  STAGE IIIB               8                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
  1P LOSS MUTATED    30  89  21   7
  1P LOSS WILD-TYPE  81 201  48  16
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              30                81
  T2              89               201
  T3              21                48
  T4               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                 N0  N1  N2  N3
  1P LOSS MUTATED    78  53  12   2
  1P LOSS WILD-TYPE 234  78  27   3
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              78               234
  N1              53                78
  N2              12                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   119   1
  1P LOSS WILD-TYPE 285   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    119    1
  1P LOSS WILD-TYPE  285    6
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0             119               285
  1               1                 6
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    29 118
  1P LOSS WILD-TYPE  98 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     29  118
  1P LOSS WILD-TYPE   98  248
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              29                98
  MALE               118               248
[1] 2 2
[1] FALSE
D42V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED                                       4
  1P LOSS WILD-TYPE                                    11
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED                                         0
  1P LOSS WILD-TYPE                                       1
                   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                                                           142
  1P LOSS WILD-TYPE                                                         328
D42V9, multiclass
                                                             clus
vv                                                            1P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG CLEAR CELL 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)             142
                                                             clus
vv                                                            1P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               328
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6 141
  1P LOSS WILD-TYPE   7 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6  141
  1P LOSS WILD-TYPE    7  339
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                6                 7
  YES             141               339
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED   121   3   2   6
  1P LOSS WILD-TYPE 273   9   2  16
D42V13, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0             121               273
  R1               3                 9
  R2               2                 2
  RX               6                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   100
  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                                 100               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  87
  1P LOSS WILD-TYPE   3 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5   87
  1P LOSS WILD-TYPE    3  222
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO              87               222
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    29  27
  1Q LOSS WILD-TYPE 252 169
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               56               421 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               169 
$`1Q LOSS MUTATED`
TCGA-21-5786 TCGA-22-4593 TCGA-22-4595 TCGA-22-4604 TCGA-22-5471 TCGA-22-5477 
       33.93        35.08        24.13        13.12        31.73        44.25 
TCGA-33-A5GW TCGA-33-AASB TCGA-34-2605 TCGA-37-4129 TCGA-39-5029 TCGA-39-5034 
        0.30         6.94        28.96         6.58        24.33        36.39 
TCGA-43-3394 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 
       27.02        11.61        12.03         9.99        13.91         0.39 
TCGA-52-7811 TCGA-56-5898 TCGA-56-6545 TCGA-56-7580 TCGA-56-7730 TCGA-56-7822 
        8.75        18.25         2.04         1.32         6.51        17.49 
TCGA-56-A49D TCGA-56-A62T TCGA-58-8392 TCGA-60-2714 TCGA-60-2719 TCGA-63-A5MB 
       20.94         2.76        16.47        50.33        42.64       102.67 
TCGA-63-A5MP TCGA-66-2791 TCGA-66-2793 TCGA-68-7755 TCGA-68-7757 TCGA-77-8128 
       25.28         5.03        10.06         2.73         6.94        37.81 
TCGA-77-8133 TCGA-77-8150 TCGA-77-A5G3 TCGA-85-6175 TCGA-85-7843 TCGA-85-8287 
       53.92        54.41       117.57         9.67         1.15         0.76 
TCGA-85-A4CN TCGA-85-A53L TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK 
       19.33        12.39        16.14        49.87        57.07        19.36 
TCGA-98-8021 TCGA-98-8023 TCGA-98-A539 TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NK-A5CR 
       30.81        21.34         3.88         2.89        14.73        83.57 
TCGA-O2-A52N TCGA-O2-A52S 
       33.07        12.72 

$`1Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       11.34        23.54        92.15        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
       86.96         6.18         2.79       154.32        49.94        27.19 
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-21-1082 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-21-5787 TCGA-21-A5DI TCGA-22-0940 
       31.63        88.11        41.69        10.82        32.19        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
        7.33        14.93         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       27.02        48.82        20.48        48.33         0.56        38.17 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 
       34.75        32.02        19.30         9.57        11.77        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       63.55        14.63         0.79        54.28        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-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       22.06         7.63       133.74        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
      103.53       151.27        14.07        54.44         1.55        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
       27.02         4.70        36.62       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 
       27.16         2.63        61.61        31.50        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        67.79        56.38         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        30.94        18.15         4.96         1.12        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
        4.04        26.43        20.91         3.95         0.43         0.39 
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-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
       47.80        74.07        44.75        68.58        55.20        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
       60.79         1.71         1.94        27.39        15.58        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       35.70        17.88        17.06        40.21        22.49        38.66 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       33.11        18.38        27.91        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
        5.46         3.81        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-51-4080 
       11.77         2.93         9.73        14.20        10.65         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-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
        0.10         0.62         0.99         0.43         0.99         1.45 
TCGA-56-7582 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.85         0.10         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
        9.93        20.25        15.81        19.23        13.32        17.85 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 
       21.04        18.74         0.13         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-60-2696 TCGA-60-2697 
       56.65        35.24        29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 
       49.48        66.54        41.42         9.01        56.91        35.34 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       48.49         3.19        32.32        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ 
       26.83        11.77        70.62        66.61        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-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       25.41        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-66-2773 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-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 
       22.98        30.02        54.08         4.01        49.05         6.64 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
        8.02        13.35        16.18        14.73        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       75.09        23.28        11.18        89.98        20.78         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       42.28        70.13       106.95         0.16        46.78        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 
        6.51        86.76        53.95        82.92        12.59        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-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        9.63        65.49        35.90         0.33       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       38.86        11.97        12.99         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        14.07        16.87        34.52 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
       10.09        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         0.72         7.76        14.63        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC 
       12.59         0.10        15.62        25.68        17.72        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        18.18        19.73        12.56        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
       14.96         0.79         3.65        24.92         9.50         2.93 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       11.77        14.07        20.22        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        3.48         4.01         5.26         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
       11.70         4.01         5.03        26.63        14.14        17.69 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 
       18.31        17.46        16.57         8.42         2.76        30.67 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       27.16        18.15         2.01        27.02        21.21        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       18.58        20.71        19.10        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       13.41        11.84         0.07        64.08         4.54        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN 
        1.22        45.37        13.74         4.21        39.85        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX 
       30.58        24.00        29.75        22.78        65.49         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       16.80         0.43         3.72        43.89         8.58        11.18 
TCGA-XC-AA0X 
        0.20 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.30              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           117.57            174.08 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            16.98             19.30 
[1] "0.3 - 117.6 (17.0)" "0.0 - 174.1 (19.3)"
[1] "hr=" "1.4"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         1        6       13        0        15        10
  1Q LOSS WILD-TYPE       1       81      138        2        48        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  1Q LOSS MUTATED           1         10          3        0
  1Q LOSS WILD-TYPE         2         52         18        7
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 6                81
  STAGE IB                13               138
  STAGE II                 0                 2
  STAGE IIA               15                48
  STAGE IIB               10                82
  STAGE III                1                 2
  STAGE IIIA              10                52
  STAGE IIIB               3                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
  1Q LOSS MUTATED    12  34  10   3
  1Q LOSS WILD-TYPE  99 256  59  20
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              12                99
  T2              34               256
  T3              10                59
  T4               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                 N0  N1  N2  N3
  1Q LOSS MUTATED    31  20   7   1
  1Q LOSS WILD-TYPE 281 111  32   4
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              31               281
  N1              20               111
  N2               7                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"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    46   0
  1Q LOSS WILD-TYPE 358   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     46    0
  1Q LOSS WILD-TYPE  358    7
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              46               358
  1               0                 7
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    11  48
  1Q LOSS WILD-TYPE 116 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   48
  1Q LOSS WILD-TYPE  116  318
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11               116
  MALE                48               318
[1] 2 2
[1] FALSE
D43V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED                                       0
  1Q LOSS WILD-TYPE                                    15
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED                                         0
  1Q LOSS WILD-TYPE                                       1
                   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                                                            58
  1Q LOSS WILD-TYPE                                                         412
D43V9, multiclass
                                                             clus
vv                                                            1Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     0
  LUNG CLEAR CELL 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)              58
                                                             clus
vv                                                            1Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      15
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               412
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  56
  1Q LOSS WILD-TYPE  10 424
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   56
  1Q LOSS WILD-TYPE   10  424
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                3                10
  YES              56               424
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    44   3   2   2
  1Q LOSS WILD-TYPE 350   9   2  20
D43V13, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              44               350
  R1               3                 9
  R2               2                 2
  RX               2                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       2                         6    40
  1Q LOSS WILD-TYPE     7                        25   300
D43V14, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               6                25
  WHITE                                  40               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"
D43V15, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2  38
  1Q LOSS WILD-TYPE   6 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   38
  1Q LOSS WILD-TYPE    6  271
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              38               271
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    12   8
  2P LOSS WILD-TYPE 269 188
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               20               457 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               188 
$`2P LOSS MUTATED`
TCGA-21-5787 TCGA-22-4594 TCGA-22-5481 TCGA-33-4533 TCGA-37-4141 TCGA-37-5819 
       10.82        48.33        79.20       133.74         0.39         3.39 
TCGA-39-5028 TCGA-39-5029 TCGA-43-2578 TCGA-51-4081 TCGA-56-8307 TCGA-66-2756 
        1.71        24.33        22.49        29.95        26.89         0.99 
TCGA-66-2763 TCGA-68-A59J TCGA-77-7465 TCGA-85-8352 TCGA-85-A511 TCGA-NC-A5HM 
        0.99        14.73        15.75         5.29        14.96        39.85 
TCGA-NC-A5HR TCGA-NK-A5CR 
       29.75        83.57 

$`2P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       11.34        23.54        92.15        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
       86.96         6.18         2.79       154.32        49.94        27.19 
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-21-1082 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-A5DI TCGA-22-0940 
       31.63        88.11        41.69        33.93        32.19        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
        7.33        14.93         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 
       27.02        48.82        20.48        35.08        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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       11.77        31.73        64.93        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        54.28        71.34        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
       62.86        56.32        16.64        22.06         7.63        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       79.53       174.08       103.53       151.27        14.07        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
        1.55        19.76        27.02         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-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
       61.61        31.50        28.96        32.88        31.27        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       67.79        56.38         9.07        23.24        12.00        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       30.94        18.15         4.96         1.12        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       26.43        20.91         3.95         0.43         0.39         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-39-5011 TCGA-39-5016 
        8.12         7.46         7.82         6.81        47.80        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 
       44.75        68.58        55.20        70.03        60.79         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
       27.39        36.39        15.58        35.64        35.70        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       17.06        40.21        38.66        27.02        33.11        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       27.91        12.36        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
       19.59         7.76        66.51        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
       11.61         9.73        14.20        12.03         9.99        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
       13.91         0.39         0.39        28.34         5.46        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         0.10        18.25         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
        0.62         0.99         0.43         0.99         1.45         1.32 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 
        0.85         6.51         0.10        17.49         3.48        17.00 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       14.07         1.35        16.77         1.81        22.75         1.18 
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-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
       13.32        17.85        21.04        18.74         0.13         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        2.76         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-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       41.42         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       42.64         3.19        32.32        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       26.83        11.77       102.67        70.62        66.61        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-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       78.28        16.37        25.41        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-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 
        2.01         0.92        43.99        21.01        25.05         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-66-2773 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-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       49.05         2.73         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       16.18        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       89.98        20.78         0.49        42.28        70.13       106.95 
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        53.95        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       82.92        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       11.54        26.40        27.39         6.97         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       65.49        35.90         0.33       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       38.86         9.67        11.97        12.99         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        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       16.87        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         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       19.33        17.72        14.96        24.36        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       12.56        16.21        15.85         0.79        12.39         3.65 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
       24.92         9.50         2.93        11.77        14.07        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-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.30        21.04         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       26.63        14.14        16.14        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       18.31        17.46        19.36        16.57         8.42         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
       30.81        30.67        21.34        27.16         3.88        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
        2.01        27.02        21.21        20.32        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       19.10        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
        0.07        64.08         4.54        51.78         1.22        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21         2.89        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE 
       14.73        22.78        65.49         3.65        16.80         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       33.07         3.72        12.72        43.89         8.58        11.18 
TCGA-XC-AA0X 
        0.20 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.39              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           133.74            174.08 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            19.12             19.10 
[1] "0.4 - 133.7 (19.1)" "0.0 - 174.1 (19.1)"
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        2        5        0         2         4
  2P LOSS WILD-TYPE       2       85      146        2        61        88
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  2P LOSS MUTATED           0          6          1        0
  2P LOSS WILD-TYPE         3         56         20        7
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                85
  STAGE IB                 5               146
  STAGE II                 0                 2
  STAGE IIA                2                61
  STAGE IIB                4                88
  STAGE III                0                 3
  STAGE IIIA               6                56
  STAGE IIIB               1                20
  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     3  12   3   2
  2P LOSS WILD-TYPE 108 278  66  21
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               3               108
  T2              12               278
  T3               3                66
  T4               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                 N0  N1  N2  N3
  2P LOSS MUTATED     9   7   4   0
  2P LOSS WILD-TYPE 303 124  35   5
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               9               303
  N1               7               124
  N2               4                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"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    18   0
  2P LOSS WILD-TYPE 386   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     18    0
  2P LOSS WILD-TYPE  386    7
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              18               386
  1               0                 7
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9  11
  2P LOSS WILD-TYPE 118 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9   11
  2P LOSS WILD-TYPE  118  355
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               9               118
  MALE                11               355
[1] 2 2
[1] FALSE
D44V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED                                       1
  2P LOSS WILD-TYPE                                    14
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED                                         0
  2P LOSS WILD-TYPE                                       1
                   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                                                            19
  2P LOSS WILD-TYPE                                                         451
D44V9, multiclass
                                                             clus
vv                                                            2P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG CLEAR CELL 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)              19
                                                             clus
vv                                                            2P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               451
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  19
  2P LOSS WILD-TYPE  12 461
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   19
  2P LOSS WILD-TYPE   12  461
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                1                12
  YES              19               461
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, continuous
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    19   0   0   0
  2P LOSS WILD-TYPE 375  12   4  22
D44V13, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              19               375
  R1               0                12
  R2               0                 4
  RX               0                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    14
  2P LOSS WILD-TYPE     9                        29   326
D44V14, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               2                29
  WHITE                                  14               326
[1] 3 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  12
  2P LOSS WILD-TYPE   7 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   12
  2P LOSS WILD-TYPE    7  297
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              12               297
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    25  15
  2Q LOSS WILD-TYPE 256 181
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               40               437 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15               181 
$`2Q LOSS MUTATED`
TCGA-18-3417 TCGA-21-1082 TCGA-21-5786 TCGA-21-5787 TCGA-22-4594 TCGA-22-4604 
       36.07       119.80        33.93        10.82        48.33        13.12 
TCGA-22-5481 TCGA-33-4533 TCGA-37-4141 TCGA-39-5028 TCGA-43-2578 TCGA-43-7657 
       79.20       133.74         0.39         1.71        22.49         7.76 
TCGA-43-8115 TCGA-51-4081 TCGA-56-8304 TCGA-56-8307 TCGA-56-A62T TCGA-58-8392 
       13.38        29.95         3.48        26.89         2.76        16.47 
TCGA-58-A46K TCGA-60-2713 TCGA-60-2724 TCGA-63-A5MH TCGA-63-A5MP TCGA-66-2763 
       34.36        56.91        23.57        66.61        25.28         0.99 
TCGA-66-2767 TCGA-66-2800 TCGA-68-A59J TCGA-77-7465 TCGA-77-8007 TCGA-77-8136 
        2.01        49.05        14.73        15.75         6.51        39.09 
TCGA-85-7696 TCGA-85-7699 TCGA-85-8288 TCGA-85-8352 TCGA-85-8664 TCGA-85-A511 
       36.53        32.91        13.22         5.29         0.10        14.96 
TCGA-94-A5I4 TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CR 
       16.14        39.85        29.75        83.57 

$`2Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 
       11.34        23.54        92.15        31.99         1.64        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
        6.18         2.79       154.32        49.94        27.19       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-21-1083 TCGA-21-5782 TCGA-21-5783 
       31.73       122.43         9.34        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       41.69        32.19        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
       64.21         1.74        14.10        27.02        48.82        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-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 
       14.63        44.25         0.79        54.28        71.34        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       18.84        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        7.63        98.01        79.53       174.08       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
       14.07        54.44         1.55        19.76        27.02         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-34-2604 TCGA-34-2605 TCGA-34-2608 
       27.16         2.63        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.27        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       12.00        16.93        30.94        18.15         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       27.19         4.04        26.43        20.91         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.39         6.58         8.12         7.46         7.82         6.81 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        3.39        47.80        74.07        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       70.03        60.79        24.33         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
       15.58        35.64        35.70        17.88        17.06        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
       38.66        27.02        33.11        18.38        27.91        12.36 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 
       24.89        21.47         5.46         3.81        19.59        66.51 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
       11.77         2.93        11.61         9.73        14.20        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
        9.99        10.65        13.91         0.39         0.39        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         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
       18.25         2.04         0.62         0.99         0.43         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
        1.45         1.32         0.85         6.51         0.10        17.49 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
       17.00        14.07         1.35        16.77         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.18        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       19.23        13.32        17.85        21.04        18.74         0.13 
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-58-8393 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-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
        3.58        12.23        10.22        96.82        37.94        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
       21.93        80.45        49.48        66.54        41.42         9.01 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       50.33        35.34        48.49        42.64         3.19        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG 
       29.85        35.90        26.83        11.77       102.67        70.62 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR 
       58.65        59.97        45.57        14.99        11.34        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       78.28        16.37        25.41        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-66-2765 TCGA-66-2766 TCGA-66-2768 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-66-2781 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-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         5.03        30.02        10.06        54.08         4.01 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
        2.73         6.64         6.94         8.02        13.35        16.18 
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        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       20.78         0.49        42.28        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
       46.78        86.76        53.95        37.81        82.92        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-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97         9.63        54.41        65.49        35.90         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       117.57        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       42.08        30.81        27.62        38.86         9.67        11.97 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 
       12.99         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-85-8350 
       14.07        16.87        34.52        10.09         0.76        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         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       14.63        13.94        12.59        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       17.72        14.96        24.36        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       16.21        15.85         0.79        12.39         3.65        24.92 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
        9.50         2.93        11.77        14.07        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-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
       21.04         0.16        11.70         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
       14.14        17.69        49.87        57.07        18.31        17.46 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       19.36        16.57         8.42         2.76        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       21.34        27.16         3.88        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       21.21        20.32        18.58        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       16.11        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        51.78         1.22        45.37        13.74         4.21 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
        2.89        37.22        30.58        24.00        14.73        22.78 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       65.49         3.65        16.80         0.43        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89         8.58        11.18         0.20 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.10              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           133.74            174.08 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            23.03             19.04 
[1] "0.1 - 133.7 (23.0)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         0        6        9        0         7         8
  2Q LOSS WILD-TYPE       2       81      142        2        56        84
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  2Q LOSS MUTATED           0          7          2        1
  2Q LOSS WILD-TYPE         3         55         19        6
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 6                81
  STAGE IB                 9               142
  STAGE II                 0                 2
  STAGE IIA                7                56
  STAGE IIB                8                84
  STAGE III                0                 3
  STAGE IIIA               7                55
  STAGE IIIB               2                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
  2Q LOSS MUTATED     7  26   4   3
  2Q LOSS WILD-TYPE 104 264  65  20
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               7               104
  T2              26               264
  T3               4                65
  T4               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                 N0  N1  N2  N3
  2Q LOSS MUTATED    19  17   3   1
  2Q LOSS WILD-TYPE 293 114  36   4
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              19               293
  N1              17               114
  N2               3                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    32   1
  2Q LOSS WILD-TYPE 372   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     32    1
  2Q LOSS WILD-TYPE  372    6
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              32               372
  1               1                 6
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    13  27
  2Q LOSS WILD-TYPE 114 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     13   27
  2Q LOSS WILD-TYPE  114  339
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              13               114
  MALE                27               339
[1] 2 2
[1] FALSE
D45V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED                                       2
  2Q LOSS WILD-TYPE                                    13
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED                                         0
  2Q LOSS WILD-TYPE                                       1
                   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                                                            38
  2Q LOSS WILD-TYPE                                                         432
D45V9, multiclass
                                                             clus
vv                                                            2Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG CLEAR CELL 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)              38
                                                             clus
vv                                                            2Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               432
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1  39
  2Q LOSS WILD-TYPE  12 441
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   39
  2Q LOSS WILD-TYPE   12  441
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                1                12
  YES              39               441
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    36   1   0   1
  2Q LOSS WILD-TYPE 358  11   4  21
D45V13, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              36               358
  R1               1                11
  R2               0                 4
  RX               1                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    27
  2Q LOSS WILD-TYPE     9                        28   313
D45V14, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               3                28
  WHITE                                  27               313
[1] 3 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  25
  2Q LOSS WILD-TYPE   8 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   25
  2Q LOSS WILD-TYPE    8  284
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              25               284
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   181 118
  3P LOSS WILD-TYPE 100  78
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              299               178 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              118                78 
$`3P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       92.15        31.99        36.07         6.18         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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
       32.19        21.99         7.33        14.10        27.02        20.48 
TCGA-22-4594 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       48.33        38.17        13.12        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 
       11.77        31.73        64.93        63.55        14.63         0.79 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5492 
       54.28        71.34        79.20        11.74        18.84        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 
       22.06         7.63       151.27        54.44         1.55        27.02 
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-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5929 
       31.50        28.96        32.88        65.23        23.24         4.96 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        4.04        26.43        20.91         6.58         8.12         7.46 
TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 
        7.82         0.39         3.39        47.80        74.07        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 
       60.79         1.71        27.39        15.58        35.64        40.21 
TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 
       38.66        33.11        12.36        21.47        19.59         7.76 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-51-4079 
       66.51        13.38        11.77         2.93        11.61         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-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
       28.96         0.10         2.04         0.99         0.43         1.45 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 
        1.32         0.85         0.10        17.49         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 
       14.07         1.35        16.77         1.18         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DS TCGA-56-A62T 
       15.81        13.32        17.85        21.04         0.26         2.76 
TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-60-2695 TCGA-60-2696 
        0.03        13.55        29.95        71.24        21.11         3.58 
TCGA-60-2698 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 
       10.22        37.94        21.93        80.45        66.54        41.42 
TCGA-60-2712 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
        9.01        42.64        32.32        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
       26.83        11.77        66.61        58.65        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MY 
       14.99        89.29        78.28        16.37        25.41        34.59 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
       43.10         2.01        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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
        6.94         8.02        13.35        16.18        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        89.98         0.49        42.28 
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        15.75        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       82.92        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         9.63        65.49        35.90         0.33       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 
       22.29         5.92        38.86         9.67        11.97         6.41 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
       34.95        31.30        32.91         1.38        29.95        18.94 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 
       24.13        31.56        14.07        16.87        10.09        13.22 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8666 
       16.77         3.09         2.01         0.72         7.76        15.62 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z 
       25.68        19.33        17.72        18.18        19.73        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
       15.85        14.96        12.39         3.65         9.50         2.93 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
       14.07        20.22        22.62        10.59         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7557 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
        5.26         2.30         0.16        26.63        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8021 
       17.69        49.87        18.31        17.46        19.36        30.81 
TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       21.34         3.88        18.15        18.58        20.71        12.89 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       13.18        11.84         0.07        64.08         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO 
       45.37        13.74         2.89        39.85        37.22        30.58 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       24.00        14.73        83.57        65.49         3.65        16.80 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
        3.72        12.72        43.89         8.58        11.18 

$`3P LOSS WILD-TYPE`
TCGA-18-3410 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-18-5595 TCGA-21-1072 
        4.80        23.54         1.64        86.96        27.19        99.16 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5784 TCGA-22-1000 
       60.89        15.58       122.43         9.34        41.69        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1017 TCGA-22-4593 TCGA-22-4595 
        4.31        64.21         1.74        48.82        35.08        24.13 
TCGA-22-4596 TCGA-22-4601 TCGA-22-5477 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        0.56        34.75        44.25        30.12        62.86        56.32 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
      133.74        98.01        79.53       174.08       103.53        14.07 
TCGA-33-6737 TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-34-2609 
       19.76         0.30         6.94       110.99       118.36        31.27 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       67.79        56.38         9.07        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       18.15         1.12        27.19         3.95         0.43         0.39 
TCGA-37-4135 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5029 TCGA-39-5030 
        6.81        44.75        68.58        55.20        24.33         1.94 
TCGA-39-5034 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 
       36.39        35.70        17.88        17.06        22.49        27.02 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-A475 
       18.38        27.91        24.89         5.46         3.81         9.73 
TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-52-7810 
       14.20        12.03         9.99        10.65        13.91        30.35 
TCGA-56-5898 TCGA-56-6546 TCGA-56-7223 TCGA-56-7730 TCGA-56-8308 TCGA-56-8622 
       18.25         0.62         0.99         6.51        17.00         1.81 
TCGA-56-8623 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DR 
       22.75        10.36        20.94        19.23        18.74         0.13 
TCGA-58-8387 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       13.25        16.47        34.78        85.12        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2703 TCGA-60-2706 TCGA-60-2709 
       35.24        29.92        12.23        96.82        92.71        49.48 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-63-A5MB 
       56.91        50.33        35.34        48.49         3.19       102.67 
TCGA-63-A5MG TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 
       70.62        11.34        25.28        36.16        53.88        16.96 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2756 TCGA-66-2759 TCGA-66-2766 TCGA-66-2771 
        0.99         1.02         0.99        25.05         1.02        19.00 
TCGA-66-2777 TCGA-66-2785 TCGA-66-2789 TCGA-66-2794 TCGA-68-A59J TCGA-77-7140 
        2.01         1.97         4.04        54.08        14.73        20.78 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8131 TCGA-77-8136 TCGA-77-8145 
        6.51        86.76        53.95        12.59        39.09         6.97 
TCGA-77-8150 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
       54.41       126.18       132.36        42.41        42.08        30.81 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 
       27.62        12.99        36.53         1.15        25.15        19.04 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 TCGA-85-8580 
       34.52         0.76        22.45         5.29        32.71        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M 
       13.94        12.59         0.10        14.96        24.36        12.56 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 TCGA-94-7033 TCGA-94-7943 
        0.79        24.92        11.77         2.70        21.04        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-96-7545 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
        4.01         5.03        57.07        16.57         8.42         2.76 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       30.67        27.16         2.01        27.02        21.21        20.32 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HR 
       19.10        16.11        13.41         1.22         4.21        29.75 
TCGA-NC-A5HT TCGA-NK-A7XE TCGA-O2-A52N TCGA-XC-AA0X 
       22.78         0.43        33.07         0.20 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.03              0.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           154.32            174.08 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            18.84             20.04 
[1] "0.0 - 154.3 (18.8)" "0.1 - 174.1 (20.0)"
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         1       53       98        1        39        54
  3P LOSS WILD-TYPE       1       34       53        1        24        38
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  3P LOSS MUTATED           3         35         14        6
  3P LOSS WILD-TYPE         0         27          7        1
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                53                34
  STAGE IB                98                53
  STAGE II                 1                 1
  STAGE IIA               39                24
  STAGE IIB               54                38
  STAGE III                3                 0
  STAGE IIIA              35                27
  STAGE IIIB              14                 7
  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
  3P LOSS MUTATED    69 181  42  15
  3P LOSS WILD-TYPE  42 109  27   8
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              69                42
  T2             181               109
  T3              42                27
  T4              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                 N0  N1  N2  N3
  3P LOSS MUTATED   197  84  21   4
  3P LOSS WILD-TYPE 115  47  18   1
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0             197               115
  N1              84                47
  N2              21                18
  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   249   6
  3P LOSS WILD-TYPE 155   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    249    6
  3P LOSS WILD-TYPE  155    1
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             249               155
  1               6                 1
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    83 224
  3P LOSS WILD-TYPE  44 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     83  224
  3P LOSS WILD-TYPE   44  142
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              83                44
  MALE               224               142
[1] 2 2
[1] FALSE
D46V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                       9
  3P LOSS WILD-TYPE                                     6
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                         0
  3P LOSS WILD-TYPE                                       1
                   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                                                           294
  3P LOSS WILD-TYPE                                                         176
D46V9, multiclass
                                                             clus
vv                                                            3P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             294
                                                             clus
vv                                                            3P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               176
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     9 298
  3P LOSS WILD-TYPE   4 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      9  298
  3P LOSS WILD-TYPE    4  182
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                9                 4
  YES             298               182
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED   244   4   3  14
  3P LOSS WILD-TYPE 150   8   1   8
D46V13, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0             244               150
  R1               4                 8
  R2               3                 1
  RX              14                 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
  3P LOSS MUTATED       3                        17   211
  3P LOSS WILD-TYPE     6                        14   129
D46V14, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              17                14
  WHITE                                 211               129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     6 181
  3P LOSS WILD-TYPE   2 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6  181
  3P LOSS WILD-TYPE    2  128
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO             181               128
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    36  30
  3Q LOSS WILD-TYPE 245 166
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               66               411 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               30               166 
$`3Q LOSS MUTATED`
TCGA-18-3408 TCGA-18-3412 TCGA-18-3416 TCGA-18-5592 TCGA-21-1075 TCGA-21-1079 
       75.75        11.34        31.99        49.94        70.16        31.73 
TCGA-21-1082 TCGA-22-0944 TCGA-22-1016 TCGA-22-4594 TCGA-22-4604 TCGA-22-5483 
      119.80         7.33        27.02        48.33        13.12        18.84 
TCGA-33-4583 TCGA-33-6738 TCGA-34-5929 TCGA-37-4129 TCGA-39-5011 TCGA-39-5027 
      151.27        27.02         4.96         6.58        47.80        60.79 
TCGA-43-2581 TCGA-43-A474 TCGA-52-7811 TCGA-56-1622 TCGA-56-7221 TCGA-56-7579 
       38.66        11.61         8.75        28.96         0.99         1.45 
TCGA-56-7582 TCGA-56-8307 TCGA-56-8503 TCGA-58-8388 TCGA-60-2696 TCGA-60-2698 
        0.85        26.89         1.35        13.55         3.58        10.22 
TCGA-60-2722 TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MU TCGA-66-2737 TCGA-66-2754 
       29.85        58.65        59.97        25.41         2.01         2.01 
TCGA-66-2757 TCGA-66-2769 TCGA-66-2782 TCGA-66-2788 TCGA-66-2791 TCGA-66-2793 
       43.99         7.07        12.00        22.98         5.03        10.06 
TCGA-66-2795 TCGA-77-6843 TCGA-77-6844 TCGA-77-8130 TCGA-77-8154 TCGA-85-6175 
        4.01        73.12        75.09        82.92        35.90         9.67 
TCGA-85-7698 TCGA-85-8070 TCGA-85-8071 TCGA-85-8481 TCGA-85-A4CN TCGA-85-A50Z 
       31.30        31.56        14.07         7.76        19.33        16.21 
TCGA-85-A53L TCGA-90-A4ED TCGA-92-7341 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-8169 
       12.39        20.22         3.48         0.16        16.14        18.31 
TCGA-98-8023 TCGA-98-A539 TCGA-NC-A5HE TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-O2-A5IB 
       21.34         3.88        64.08         2.89        14.73        11.18 

$`3Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
       12.20         7.46        79.46         4.80       117.57        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       92.15        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 
      154.32        27.19       119.54        46.88        99.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 
       34.78        15.58       122.43         9.34        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
       88.11        41.69        33.93        10.82        32.19        21.99 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 
       14.93         4.31        64.21         1.74        14.10        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       20.48        35.08        24.13         0.56        38.17        34.75 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       32.02        19.30         9.57        11.77        31.73        64.93 
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        54.28        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-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       22.06         7.63       133.74        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-A4WN 
      103.53        14.07        54.44         1.55        19.76         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-34-2604 TCGA-34-2605 TCGA-34-2608 
       27.16         2.63        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.27        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 
       12.00        16.93        30.94        18.15         1.12        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
        4.04        26.43        20.91         3.95         0.43         0.39 
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-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
       74.07        44.75        68.58        55.20        70.03         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        27.39        36.39        15.58        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 
       35.70        17.88        17.06        40.21        22.49        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       33.11        18.38        27.91        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
        5.46         3.81        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
       11.77         2.93         9.73        14.20        12.03         9.99 
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-56-6545 
        5.46        30.35        27.45         0.10        18.25         2.04 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
        0.62         0.43         0.99         1.32         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 
       17.49         3.48        17.00        14.07        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.94        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 
        0.13         0.26         2.76         0.03        13.25        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-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       92.71        21.93        80.45        49.48        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
        9.01        56.91        50.33        35.34        48.49        42.64 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
        3.19        32.32        35.90        23.57        26.83        11.77 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
      102.67        70.62        66.61        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-66-2742 TCGA-66-2744 TCGA-66-2753 
       34.59        16.96        43.10        21.07         0.99         1.02 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.92         0.99        21.01        25.05         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-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 
        2.01        19.00        12.03         3.98        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 
       25.97        40.01         4.04        22.98        30.02        54.08 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       49.05         2.73         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       16.18        14.73        29.56        23.28        11.18        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       20.78         0.49        42.28        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        15.75         6.51        86.76        53.95        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         9.63        54.41        65.49 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        0.33       126.18       132.36       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
       42.41        42.08        30.81        27.62        38.86        11.97 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
       12.99         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-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       16.87        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         0.72 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       17.72        14.96        24.36        18.18        19.73        12.56 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       15.85        14.96         0.79         3.65        24.92         9.50 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        2.93        11.77        14.07        22.62        10.59         2.70 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-8035 
        4.01         5.26         2.30        21.04        11.70         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
        5.03        26.63        14.14        17.69        49.87        57.07 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 
       17.46        19.36        16.57         8.42         2.76        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       30.67        27.16        18.15         2.01        27.02        21.21 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
       20.32        18.58        20.71        19.10        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG 
       13.18        13.41        11.84         0.07         4.54        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN 
        1.22        45.37        13.74         4.21        39.85        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       30.58        24.00        29.75        22.78        83.57        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
        3.65        16.80         0.43        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       43.89         8.58         0.20 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.16              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           151.27            174.08 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            17.26             19.30 
[1] "0.2 - 151.3 (17.3)" "0.0 - 174.1 (19.3)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         0        8       17        0        10        17
  3Q LOSS WILD-TYPE       2       79      134        2        53        75
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  3Q LOSS MUTATED           1         11          4        0
  3Q LOSS WILD-TYPE         2         51         17        7
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 8                79
  STAGE IB                17               134
  STAGE II                 0                 2
  STAGE IIA               10                53
  STAGE IIB               17                75
  STAGE III                1                 2
  STAGE IIIA              11                51
  STAGE IIIB               4                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
  3Q LOSS MUTATED    12  37  17   3
  3Q LOSS WILD-TYPE  99 253  52  20
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              12                99
  T2              37               253
  T3              17                52
  T4               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                 N0  N1  N2  N3
  3Q LOSS MUTATED    40  23   5   1
  3Q LOSS WILD-TYPE 272 108  34   4
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              40               272
  N1              23               108
  N2               5                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"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    63   0
  3Q LOSS WILD-TYPE 341   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     63    0
  3Q LOSS WILD-TYPE  341    7
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              63               341
  1               0                 7
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    14  55
  3Q LOSS WILD-TYPE 113 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     14   55
  3Q LOSS WILD-TYPE  113  311
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              14               113
  MALE                55               311
[1] 2 2
[1] FALSE
D47V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED                                       1
  3Q LOSS WILD-TYPE                                    14
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED                                         0
  3Q LOSS WILD-TYPE                                       1
                   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                                                            66
  3Q LOSS WILD-TYPE                                                         404
D47V9, multiclass
                                                             clus
vv                                                            3Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              66
                                                             clus
vv                                                            3Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               404
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  68
  3Q LOSS WILD-TYPE  12 412
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   68
  3Q LOSS WILD-TYPE   12  412
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                1                12
  YES              68               412
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    56   2   0   4
  3Q LOSS WILD-TYPE 338  10   4  18
D47V13, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              56               338
  R1               2                10
  R2               0                 4
  RX               4                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
  3Q LOSS MUTATED       2                         2    46
  3Q LOSS WILD-TYPE     7                        29   294
D47V14, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               2                29
  WHITE                                  46               294
[1] 3 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  39
  3Q LOSS WILD-TYPE   7 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   39
  3Q LOSS WILD-TYPE    7  270
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              39               270
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   182 117
  4P LOSS WILD-TYPE  99  79
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              299               178 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              117                79 
$`4P LOSS MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 
        7.46       117.57        11.34        92.15        36.07        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        6.18         2.79        49.94       119.54        46.88        99.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       60.89        34.78        31.73       122.43         9.34       119.80 
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-22-1000 TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
       14.93         1.74        14.10        35.08        48.33        24.13 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 
       38.17        13.12        32.02        19.30         9.57        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 
       64.93        63.55        14.63        44.25        54.28        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4533 
       18.84        30.12        62.86        56.32         7.63       133.74 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       98.01        79.53       103.53       151.27        14.07        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB 
        1.55        19.76        27.02         4.70        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2605 
      110.99        44.19       118.36        27.16        61.61        28.96 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       65.23        67.79         9.07        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 
        4.96         1.12        26.43         3.95         0.43         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        6.81         0.39         3.39        74.07        44.75        68.58 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 
       60.79        27.39        36.39        15.58        35.70        17.06 
TCGA-43-2578 TCGA-43-3394 TCGA-43-6143 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       22.49        27.02        12.36         5.46         3.81        19.59 
TCGA-43-7657 TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
        7.76        13.38         2.93        11.61        14.20        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
        9.99        10.65        13.91        29.95         5.46        30.35 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 
        8.75        27.45        18.25         2.04         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8308 
        0.99         1.45         0.85         6.51         3.48        17.00 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T 
       20.94        19.23        13.32        18.74         0.13         2.76 
TCGA-58-8387 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       13.25        16.47        34.78        85.12        34.36        56.65 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 
       35.24        21.11         3.58        10.22        96.82        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
       21.93        80.45        49.48        66.54        41.42         9.01 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
       56.91        50.33        42.64         3.19        32.32        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ 
       35.90        23.57        11.77       102.67        66.61        59.97 
TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       45.57        89.29        78.28        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2758 TCGA-66-2759 
        2.01        21.07         1.02         2.01        21.01        25.05 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01         2.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 
       12.03         3.98        24.95         1.97        25.97         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-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
        6.64        14.73        73.12        23.28        89.98         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
       42.28        70.13        46.78        15.75        53.95        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       82.92        53.92        17.72        27.39         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
       54.41        65.49        35.90       117.57         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
       42.08        30.81        27.62        38.86        11.97        12.99 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 
       36.53        34.95        31.30        32.91         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        14.07        16.87        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 
       10.09         0.76        13.22        22.45         5.29         3.09 
TCGA-85-8354 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       32.71        14.63         0.10        15.62        25.68        19.33 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 
       18.18        19.73        15.85        12.39         3.65         9.50 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       14.07        20.22        22.62        10.59         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 
        4.01         5.26         2.30         0.16        11.70         4.01 
TCGA-94-8490 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8020 
        5.03        16.14        17.69        19.36         8.42         2.76 
TCGA-98-8021 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I 
       30.81        27.16         3.88        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-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ 
        0.07        64.08         4.54        51.78        45.37        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
        4.21         2.89        39.85        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       14.73        29.75        83.57        65.49         3.65        16.80 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89         8.58        11.18         0.20 

$`4P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
       12.20        75.75        79.46         4.80        23.54        31.99 
TCGA-18-3419 TCGA-18-4721 TCGA-18-5595 TCGA-21-1075 TCGA-21-1078 TCGA-21-5783 
        1.64       154.32        27.19        70.16        15.58        88.11 
TCGA-21-5784 TCGA-21-A5DI TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 
       41.69        32.19         4.31        64.21        27.02        48.82 
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-22-A5C4 TCGA-33-4566 TCGA-33-A5GW TCGA-34-2596 
       79.20        16.64        22.06       174.08         0.30         2.63 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
       31.50        32.88        31.27        56.38        23.24        12.00 
TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       27.19         4.04        20.91         0.39         6.58         8.12 
TCGA-37-4132 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
        7.46        47.80        55.20        70.03         1.71        24.33 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 
        1.94        35.64        17.88        40.21        38.66        33.11 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-7658 TCGA-43-8116 
       18.38        27.91        24.89        21.47        66.51        11.77 
TCGA-43-A475 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-56-1622 TCGA-56-5897 
        9.73         0.39         0.39        28.34        28.96         0.10 
TCGA-56-6546 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 
        0.62         1.32         0.10        17.49        26.89        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DS 
        9.93        20.25        15.81        17.85        21.04         0.26 
TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46N TCGA-60-2697 
        0.03        13.55        29.95        71.24        29.92        12.23 
TCGA-60-2704 TCGA-60-2715 TCGA-60-2716 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MI 
       37.94        35.34        48.49        26.83        70.62        58.65 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV 
       14.99        11.34        25.28        16.37        25.41        36.16 
TCGA-63-A5MW TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 
       53.88         0.99         0.92         0.99        43.99         0.99 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 TCGA-66-2787 
        1.02         2.01         7.07        23.01        12.00        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       22.98         4.04        22.98         6.94         8.02        13.35 
TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7140 TCGA-77-7337 
       16.18        29.56        75.09        11.18        20.78       106.95 
TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 
        0.16         6.51        86.76        12.59        39.09       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
       11.54        26.40         0.33       126.18       132.36        22.29 
TCGA-85-6175 TCGA-85-6798 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8351 
        9.67         6.41         1.38        29.95        18.94        16.77 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB 
        2.01         0.72         7.76        13.94        12.59        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 
       14.96        24.36        12.56        16.21        14.96         0.79 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-94-7033 TCGA-94-8491 TCGA-94-A4VJ 
       24.92         2.93        11.77        21.04        26.63        14.14 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8022 
       49.87        57.07        18.31        17.46        16.57        30.67 
TCGA-98-8023 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH TCGA-NC-A5HH 
       21.34        27.02        21.21        20.32        19.10         1.22 
TCGA-NC-A5HT TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       22.78         0.43        33.07         3.72 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.07              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           151.27            174.08 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            19.30             18.66 
[1] "0.1 - 151.3 (19.3)" "0.0 - 174.1 (18.7)"
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         1       50      105        2        43        50
  4P LOSS WILD-TYPE       1       37       46        0        20        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  4P LOSS MUTATED           2         38         14        3
  4P LOSS WILD-TYPE         1         24          7        4
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                50                37
  STAGE IB               105                46
  STAGE II                 2                 0
  STAGE IIA               43                20
  STAGE IIB               50                42
  STAGE III                2                 1
  STAGE IIIA              38                24
  STAGE IIIB              14                 7
  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    65 192  41  12
  4P LOSS WILD-TYPE  46  98  28  11
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              65                46
  T2             192                98
  T3              41                28
  T4              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                 N0  N1  N2  N3
  4P LOSS MUTATED   194  83  26   4
  4P LOSS WILD-TYPE 118  48  13   1
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0             194               118
  N1              83                48
  N2              26                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   254   3
  4P LOSS WILD-TYPE 150   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    254    3
  4P LOSS WILD-TYPE  150    4
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             254               150
  1               3                 4
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    76 234
  4P LOSS WILD-TYPE  51 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     76  234
  4P LOSS WILD-TYPE   51  132
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              76                51
  MALE               234               132
[1] 2 2
[1] FALSE
D48V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                       9
  4P LOSS WILD-TYPE                                     6
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                         0
  4P LOSS WILD-TYPE                                       1
                   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                                                           299
  4P LOSS WILD-TYPE                                                         171
D48V9, multiclass
                                                             clus
vv                                                            4P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             299
                                                             clus
vv                                                            4P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               171
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    11 299
  4P LOSS WILD-TYPE   2 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11  299
  4P LOSS WILD-TYPE    2  181
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               11                 2
  YES             299               181
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, continuous
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED   248   7   4  14
  4P LOSS WILD-TYPE 146   5   0   8
D48V13, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0             248               146
  R1               7                 5
  R2               4                 0
  RX              14                 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
  4P LOSS MUTATED       3                        23   216
  4P LOSS WILD-TYPE     6                         8   124
D48V14, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              23                 8
  WHITE                                 216               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     5 191
  4P LOSS WILD-TYPE   3 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5  191
  4P LOSS WILD-TYPE    3  118
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             191               118
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   169 113
  4Q LOSS WILD-TYPE 112  83
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              282               195 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              113                83 
$`4Q LOSS MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-4083 
        7.46       117.57        11.34        92.15        36.07         6.18 
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-21-1079 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-21-5786 TCGA-21-5787 TCGA-22-0944 
      119.80        43.23        31.63        33.93        10.82         7.33 
TCGA-22-1000 TCGA-22-1011 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
       14.93         1.74        14.10        48.33        24.13        38.17 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       13.12        32.02        19.30        11.77        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       63.55        14.63        54.28        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
       62.86        56.32         7.63       133.74        98.01       174.08 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
      103.53       151.27        14.07        54.44         1.55        19.76 
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-34-2605 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       61.61        28.96         9.07        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-7107 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        4.96         1.12         7.82         6.81         0.39         3.39 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
       44.75        68.58        60.79        27.39        36.39        15.58 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 TCGA-43-6143 
       35.64        35.70        17.06        22.49        27.02        12.36 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8118 
        5.46         3.81         7.76        66.51        13.38         2.93 
TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       11.61        14.20        12.03         9.99        10.65        13.91 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-5898 
        0.39        29.95         5.46        30.35         8.75        18.25 
TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 
        2.04         0.99         0.43         0.99         0.85         6.51 
TCGA-56-8304 TCGA-56-8308 TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX 
        3.48        17.00        10.36        15.81        20.94        13.32 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8390 TCGA-58-8392 
       21.04        18.74         0.13         2.76        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-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
        3.58        10.22        96.82        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
       49.48         9.01        56.91        50.33        42.64         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB 
       32.32        29.85        35.90        23.57        11.77       102.67 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS 
       70.62        66.61        59.97        45.57        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
       16.37        53.88        34.59        16.96        43.10         2.01 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 
       21.07         1.02         2.01        43.99        21.01         0.99 
TCGA-66-2765 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        2.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2785 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        3.98         1.97         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-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       14.73        73.12        23.28        89.98         0.49        42.28 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       46.78        15.75         6.51        53.95        37.81        82.92 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       53.92        39.09        17.72        27.39         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       54.41        65.49        35.90       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
       42.41        42.08        30.81        27.62        38.86        11.97 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-8048 TCGA-85-8049 
       12.99         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        16.87        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         0.72        14.63         0.10 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
       15.62        25.68        19.33        18.18        19.73        15.85 
TCGA-85-A53L TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       12.39        11.77        14.07        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7557 TCGA-94-7943 
        2.70         4.01         5.26         2.30         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-7454 
        4.01         5.03        16.14        17.69        19.36         8.42 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B TCGA-98-A53I 
       30.81        30.67        27.16         3.88         2.01        18.58 
TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       20.71        16.11        13.18        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
        4.54        45.37        13.74         4.21         2.89        39.85 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CT 
       30.58        24.00        14.73        29.75        83.57        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
        3.65        16.80        12.72        43.89         8.58         0.20 

$`4Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
       12.20        75.75        79.46         4.80        23.54        31.99 
TCGA-18-3419 TCGA-18-3421 TCGA-18-5595 TCGA-21-1078 TCGA-21-5783 TCGA-21-5784 
        1.64        86.96        27.19        15.58        88.11        41.69 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 
       32.19        21.99         4.31        64.21        27.02        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-4609 TCGA-22-5477 
       20.48        35.08         0.56        34.75         9.57        44.25 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4547 
        0.79        71.34        79.20        16.64        22.06        79.53 
TCGA-33-6738 TCGA-33-A5GW TCGA-33-AASD TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 
       27.02         0.30       110.99         2.63        31.50        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
       31.27        65.23        67.79        56.38        23.24        12.00 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       27.19         4.04        26.43        20.91         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5016 
        0.39         6.58         8.12         7.46        47.80        74.07 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5039 
       55.20        70.03         1.71        24.33         1.94        17.88 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
       40.21        38.66        33.11        18.38        27.91        24.89 
TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 TCGA-43-A475 TCGA-51-4080 TCGA-52-7622 
       21.47        19.59        11.77         9.73         0.39        28.34 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 
       27.45        28.96         0.10         0.62         1.45         1.32 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
        0.10        17.49        26.89        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW 
        1.81        22.75         1.18         9.93        20.25        19.23 
TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 
       17.85         0.26         0.03        13.25        13.55        71.24 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2704 TCGA-60-2710 TCGA-60-2711 TCGA-60-2715 
       29.92        12.23        37.94        66.54        41.42        35.34 
TCGA-60-2716 TCGA-60-2725 TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       48.49        26.83        58.65        14.99        11.34        25.28 
TCGA-63-A5MU TCGA-63-A5MV TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2759 
       25.41        36.16         0.99         0.92         0.99        25.05 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 
        1.02         2.01         2.01         7.07        23.01        12.00 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       24.95        25.97        40.01        22.98         4.04        22.98 
TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7140 
        8.02        13.35        29.56        75.09        11.18        20.78 
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         0.33       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 
       14.07        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 
       13.94        12.59        17.72        14.96        24.36        12.56 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       16.21        14.96         0.79         3.65        24.92         9.50 
TCGA-90-7767 TCGA-92-7341 TCGA-94-7033 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 
        2.93         3.48        21.04        26.63        14.14        49.87 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8020 TCGA-98-8023 
       57.07        18.31        17.46        16.57         2.76        21.34 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH TCGA-L3-A4E7 
       18.15        27.02        21.21        20.32        19.10        12.89 
TCGA-LA-A7SW TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HN TCGA-NC-A5HT TCGA-NK-A7XE 
       13.41        51.78         1.22        37.22        22.78         0.43 
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 
           174.08            132.36 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            19.00             19.59 
[1] "0.1 - 174.1 (19.0)" "0.0 - 132.4 (19.6)"
[1] "hr=" "1.2"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         1       48      103        2        33        53
  4Q LOSS WILD-TYPE       1       39       48        0        30        39
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  4Q LOSS MUTATED           1         35         11        3
  4Q LOSS WILD-TYPE         2         27         10        4
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                48                39
  STAGE IB               103                48
  STAGE II                 2                 0
  STAGE IIA               33                30
  STAGE IIB               53                39
  STAGE III                1                 2
  STAGE IIIA              35                27
  STAGE IIIB              11                10
  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    58 183  40  11
  4Q LOSS WILD-TYPE  53 107  29  12
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              58                53
  T2             183               107
  T3              40                29
  T4              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                 N0  N1  N2  N3
  4Q LOSS MUTATED   191  76  20   2
  4Q LOSS WILD-TYPE 121  55  19   3
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0             191               121
  N1              76                55
  N2              20                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   239   3
  4Q LOSS WILD-TYPE 165   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    239    3
  4Q LOSS WILD-TYPE  165    4
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             239               165
  1               3                 4
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    76 216
  4Q LOSS WILD-TYPE  51 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     76  216
  4Q LOSS WILD-TYPE   51  150
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              76                51
  MALE               216               150
[1] 2 2
[1] FALSE
D49V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                       7
  4Q LOSS WILD-TYPE                                     8
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                         0
  4Q LOSS WILD-TYPE                                       1
                   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                                                           282
  4Q LOSS WILD-TYPE                                                         188
D49V9, multiclass
                                                             clus
vv                                                            4Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             282
                                                             clus
vv                                                            4Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    11 281
  4Q LOSS WILD-TYPE   2 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     11  281
  4Q LOSS WILD-TYPE    2  199
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               11                 2
  YES             281               199
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED   232   7   3  16
  4Q LOSS WILD-TYPE 162   5   1   6
D49V13, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             232               162
  R1               7                 5
  R2               3                 1
  RX              16                 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   198
  4Q LOSS WILD-TYPE     5                        11   142
D49V14, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              20                11
  WHITE                                 198               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     4 177
  4Q LOSS WILD-TYPE   4 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4  177
  4Q LOSS WILD-TYPE    4  132
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO             177               132
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    46  25
  5P LOSS WILD-TYPE 235 171
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               71               406 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               25               171 
$`5P LOSS MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-21-1070 TCGA-21-1079 TCGA-22-4607 
       79.46         4.80         6.18       119.54        31.73        19.30 
TCGA-22-5472 TCGA-22-5479 TCGA-22-5485 TCGA-22-5491 TCGA-33-4532 TCGA-33-4538 
       64.93        54.28        30.12        56.32         7.63        98.01 
TCGA-33-4547 TCGA-33-6737 TCGA-33-A5GW TCGA-34-2605 TCGA-34-5231 TCGA-37-4130 
       79.53        19.76         0.30        28.96        65.23         8.12 
TCGA-39-5037 TCGA-43-2578 TCGA-43-8118 TCGA-51-4079 TCGA-52-7810 TCGA-56-5897 
       35.70        22.49         2.93         0.39        30.35         0.10 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7730 TCGA-56-8622 TCGA-56-A49D TCGA-58-A46L 
       18.25         0.99         6.51         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-A5MT TCGA-63-A5MY TCGA-66-2734 TCGA-66-2755 TCGA-66-2785 TCGA-66-2789 
       16.37        34.59        43.10         0.92         1.97         4.04 
TCGA-66-2791 TCGA-66-2793 TCGA-68-8250 TCGA-68-8251 TCGA-77-7139 TCGA-77-8140 
        5.03        10.06         8.02        13.35        89.98        11.54 
TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-85-6561 TCGA-85-7698 TCGA-85-7950 
        9.63        65.49        35.90        12.99        31.30        18.94 
TCGA-85-8276 TCGA-85-8288 TCGA-85-8352 TCGA-85-8355 TCGA-90-7964 TCGA-92-8063 
       34.52        13.22         5.29         2.01        14.07         4.01 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A5I4 TCGA-98-A538 TCGA-LA-A7SW TCGA-NC-A5HG 
       21.04        11.70        16.14        27.16        13.41        51.78 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HR TCGA-O2-A52S 
       45.37         2.89        39.85        29.75        12.72 

$`5P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20         7.46        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       92.15        31.99        36.07         1.64        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      154.32        49.94        27.19        46.88        99.16        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-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
       43.23        31.63        88.11        41.69        33.93        10.82 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       32.19        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
        1.74        14.10        27.02        48.82        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-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 
       32.02         9.57        11.77        31.73        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       44.25         0.79        71.34        79.20        11.74        18.84 
TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 
       62.86        16.64        22.06       133.74       174.08       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN 
      151.27        14.07        54.44         1.55        27.02         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-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 
        2.63        61.61        31.50        32.88        31.27        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       56.38         9.07        23.24        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       18.15         4.96         1.12        27.19         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
       20.91         3.95         0.43         0.39         6.58         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        47.80        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
       44.75        68.58        55.20        70.03        60.79         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        27.39        36.39        15.58        35.64 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       17.88        17.06        40.21        38.66        27.02        33.11 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       18.38        27.91        12.36        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        3.81        19.59         7.76        66.51        13.38        11.77 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
       11.61         9.73        14.20        12.03         9.99        10.65 
TCGA-46-6026 TCGA-51-4080 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-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 
       27.45        28.96         2.04         0.62         0.43         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        1.45         1.32         0.85         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8623 
       26.89        17.00        14.07         1.35        16.77        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
        1.18        10.36         9.93        20.25        15.81        19.23 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
       13.32        17.85        21.04        18.74         0.13         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        2.76         0.03        13.25        13.55        29.95        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-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       21.11         3.58        12.23        10.22        96.82        37.94 
TCGA-60-2709 TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       49.48        41.42         9.01        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        32.32        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ 
       11.77       102.67        70.62        66.61        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-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 
       25.41        36.16        53.88        16.96         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-66-2766 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-66-2786 TCGA-66-2787 
       12.03         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-77-6842 
        2.73         6.64         6.94        16.18        14.73        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 
       73.12        75.09        23.28        11.18        20.78         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       42.28        70.13       106.95         0.16        46.78        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        6.51        86.76        53.95        37.81        82.92        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8144 
       53.92        39.09        17.72       104.09        26.40        27.39 
TCGA-77-8145 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        6.97        54.41         0.33       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       38.86         9.67        11.97         6.41        36.53        34.95 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 
       32.91         1.38         1.15        29.95        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        14.07        16.87        10.09         0.76 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 
       22.45        16.77         3.09        32.71         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       19.33        17.72        14.96        24.36        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       12.56        16.21        15.85        14.96         0.79        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
        3.65        24.92         9.50         2.93        11.77        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 
       22.62        10.59         2.70         3.48         5.26         2.30 
TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        0.16         4.01         5.03        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       49.87        57.07        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 
        8.42         2.76        30.81        30.67        21.34         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
       18.15         2.01        27.02        21.21        20.32        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
       20.71        19.10        12.89        16.11        13.18        11.84 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
        0.07        64.08         4.54         1.22        13.74         4.21 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       37.22        30.58        24.00        14.73        22.78        83.57 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       65.49         3.65        16.80         0.43        33.07         3.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89         8.58        11.18         0.20 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.10              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           119.54            174.08 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            19.76             19.02 
[1] "0.1 - 119.5 (19.8)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.2"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         0       15       21        0        11         9
  5P LOSS WILD-TYPE       2       72      130        2        52        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  5P LOSS MUTATED           1         12          4        0
  5P LOSS WILD-TYPE         2         50         17        7
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                15                72
  STAGE IB                21               130
  STAGE II                 0                 2
  STAGE IIA               11                52
  STAGE IIB                9                83
  STAGE III                1                 2
  STAGE IIIA              12                50
  STAGE IIIB               4                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
  5P LOSS MUTATED    24  37  10   4
  5P LOSS WILD-TYPE  87 253  59  19
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              24                87
  T2              37               253
  T3              10                59
  T4               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                 N0  N1  N2  N3
  5P LOSS MUTATED    46  18   7   2
  5P LOSS WILD-TYPE 266 113  32   3
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              46               266
  N1              18               113
  N2               7                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    62   0
  5P LOSS WILD-TYPE 342   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     62    0
  5P LOSS WILD-TYPE  342    7
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              62               342
  1               0                 7
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    15  60
  5P LOSS WILD-TYPE 112 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     15   60
  5P LOSS WILD-TYPE  112  306
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              15               112
  MALE                60               306
[1] 2 2
[1] FALSE
D50V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED                                       4
  5P LOSS WILD-TYPE                                    11
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED                                         0
  5P LOSS WILD-TYPE                                       1
                   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                                                            70
  5P LOSS WILD-TYPE                                                         400
D50V9, multiclass
                                                             clus
vv                                                            5P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG CLEAR CELL 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)              70
                                                             clus
vv                                                            5P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               400
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     4  71
  5P LOSS WILD-TYPE   9 409
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4   71
  5P LOSS WILD-TYPE    9  409
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                4                 9
  YES              71               409
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, continuous
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    55   3   0   6
  5P LOSS WILD-TYPE 339   9   4  16
D50V13, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              55               339
  R1               3                 9
  R2               0                 4
  RX               6                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    53
  5P LOSS WILD-TYPE     8                        27   287
D50V14, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               4                27
  WHITE                                  53               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"
D50V15, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  44
  5P LOSS WILD-TYPE   5 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   44
  5P LOSS WILD-TYPE    5  265
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              44               265
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   165 109
  5Q LOSS WILD-TYPE 116  87
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              274               203 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              109                87 
$`5Q LOSS MUTATED`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       75.75        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       92.15        31.99        36.07         6.18         2.79       154.32 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1079 TCGA-21-1082 TCGA-21-5784 
      119.54        99.16        70.16        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-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5485 TCGA-22-5491 TCGA-33-4532 
       14.63        44.25        54.28        30.12        56.32         7.63 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-4587 TCGA-33-6737 
      133.74        98.01        79.53        14.07        54.44        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI 
       27.02         4.70         0.30        36.62       110.99        44.19 
TCGA-33-AASJ TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
      118.36        61.61        31.50        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5239 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       65.23        23.24        30.94         4.96         1.12        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        4.04        26.43         8.12         7.46         7.82         6.81 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 
       47.80        74.07        70.03        60.79        24.33         1.94 
TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       27.39        35.64        35.70        40.21        22.49        38.66 
TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 
       27.02        18.38        27.91        24.89        21.47         3.81 
TCGA-43-7656 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-46-3768 
       19.59        11.77         2.93        11.61        14.20         9.99 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 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-52-7811 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 
       30.35         8.75         0.10        18.25         0.62         0.99 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        1.45         0.85         6.51         0.10        17.49         3.48 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8622 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
       17.00        14.07         1.81        10.36        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       20.94        13.32        17.85        21.04        18.74         0.13 
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-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 TCGA-60-2706 
       85.12        34.36        56.65        21.11         3.58        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
       21.93        80.45        49.48        66.54        41.42        56.91 
TCGA-60-2714 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MB 
       50.33         3.19        32.32        29.85        35.90       102.67 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       59.97        45.57        25.28        78.28        16.37        25.41 
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-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 
        1.02         0.92         0.99        43.99        25.05         0.99 
TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 
        1.02         7.07         3.02         2.01        12.03         3.98 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
       12.00         1.97        40.01        22.98         4.04         5.03 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       10.06        54.08        49.05         2.73         6.64         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 TCGA-77-8007 
        8.02        13.35        89.98         0.49         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         9.63        65.49        35.90       117.57        42.41 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 
       38.86        11.97        12.99         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        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
       16.87        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        14.63 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A511 
       15.62        19.33        17.72        14.96        19.73        14.96 
TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE TCGA-92-8063 
        3.65         9.50         2.93        14.07        22.62         4.01 
TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        5.26        21.04         0.16        11.70         4.01         5.03 
TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 
       16.14        49.87        57.07        19.36        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-L3-A524 
       21.34        27.16         3.88        18.15         2.01        16.11 
TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ 
       13.41         0.07         4.54        51.78        45.37        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NK-A5CT 
        4.21         2.89        39.85        24.00        29.75        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52S TCGA-O2-A52W 
        3.65        16.80        12.72         8.58 

$`5Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3419 TCGA-18-3421 TCGA-18-5592 TCGA-18-5595 
       12.20         7.46         1.64        86.96        49.94        27.19 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
       46.88        60.89        34.78        15.58       122.43         9.34 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1005 
       43.23        31.63        88.11        32.19        14.93        64.21 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       14.10        27.02        48.82        48.33        24.13         0.56 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 
        0.79        71.34        79.20        11.74        18.84        62.86 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4589 
       16.64        22.06       174.08       103.53       151.27         1.55 
TCGA-33-AASB TCGA-33-AASL TCGA-34-2596 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
        6.94        27.16         2.63        67.79        56.38         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       12.00        16.93        18.15        20.91         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 
        0.39         6.58         0.39         3.39        44.75        68.58 
TCGA-39-5022 TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 
       55.20         1.71        36.39        15.58        17.88        17.06 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       33.11        12.36         5.46         7.76        66.51        13.38 
TCGA-43-A475 TCGA-43-A56V TCGA-51-4080 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 
        9.73        12.03         0.39        27.45        28.96         2.04 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-8307 TCGA-56-8503 TCGA-56-8504 
        0.43         0.99         1.32        26.89         1.35        16.77 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A62T TCGA-58-8386 
       22.75         1.18         9.93        19.23         2.76         0.03 
TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       34.78        35.24        29.92        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2724 
       37.94         9.01        35.34        48.49        42.64        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM 
       26.83        11.77        70.62        66.61        58.65        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MV TCGA-66-2744 TCGA-66-2754 TCGA-66-2758 
       11.34        89.29        36.16         0.99         2.01        21.01 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 
        2.01         2.01         2.01        23.01        19.00        19.00 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2790 TCGA-66-2792 TCGA-66-2795 TCGA-68-A59I 
       24.95        25.97        22.98        30.02         4.01        16.18 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       14.73        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7140 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 
       20.78        42.28        70.13       106.95        46.78        15.75 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8144 
       86.76        53.95        82.92        12.59        53.92        27.39 
TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
       54.41         0.33       126.18       132.36        22.29         5.92 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6175 TCGA-85-7696 TCGA-85-7699 
       42.08        30.81        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         0.72        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       12.59         0.10        25.68        24.36        18.18        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 
       16.21        15.85         0.79        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        16.57         8.42 
TCGA-98-8020 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
        2.76        27.02        21.21        20.32        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HH 
       19.10        12.89        13.18        11.84        64.08         1.22 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A7XE 
       37.22        30.58        14.73        22.78        83.57         0.43 
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            174.08 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            19.12             19.10 
[1] "0.1 - 154.3 (19.1)" "0.0 - 174.1 (19.1)"
[1] "hr=" "1"  
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         1       51       89        1        36        47
  5Q LOSS WILD-TYPE       1       36       62        1        27        45
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  5Q LOSS MUTATED           1         38         13        6
  5Q LOSS WILD-TYPE         2         24          8        1
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                51                36
  STAGE IB                89                62
  STAGE II                 1                 1
  STAGE IIA               36                27
  STAGE IIB               47                45
  STAGE III                1                 2
  STAGE IIIA              38                24
  STAGE IIIB              13                 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    67 166  36  16
  5Q LOSS WILD-TYPE  44 124  33   7
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              67                44
  T2             166               124
  T3              36                33
  T4              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                 N0  N1  N2  N3
  5Q LOSS MUTATED   189  69  23   2
  5Q LOSS WILD-TYPE 123  62  16   3
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0             189               123
  N1              69                62
  N2              23                16
  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   228   6
  5Q LOSS WILD-TYPE 176   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    228    6
  5Q LOSS WILD-TYPE  176    1
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0             228               176
  1               6                 1
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    71 214
  5Q LOSS WILD-TYPE  56 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     71  214
  5Q LOSS WILD-TYPE   56  152
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              71                56
  MALE               214               152
[1] 2 2
[1] FALSE
D51V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                      10
  5Q LOSS WILD-TYPE                                     5
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                         0
  5Q LOSS WILD-TYPE                                       1
                   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                                                           272
  5Q LOSS WILD-TYPE                                                         198
D51V9, multiclass
                                                             clus
vv                                                            5Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             272
                                                             clus
vv                                                            5Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               198
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    10 275
  5Q LOSS WILD-TYPE   3 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     10  275
  5Q LOSS WILD-TYPE    3  205
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               10                 3
  YES             275               205
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED   225   8   2  14
  5Q LOSS WILD-TYPE 169   4   2   8
D51V13, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0             225               169
  R1               8                 4
  R2               2                 2
  RX              14                 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                        20   198
  5Q LOSS WILD-TYPE     6                        11   142
D51V14, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              20                11
  WHITE                                 198               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     6 180
  5Q LOSS WILD-TYPE   2 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6  180
  5Q LOSS WILD-TYPE    2  129
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO             180               129
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    60  46
  6P LOSS WILD-TYPE 221 150
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              106               371 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               46               150 
$`6P LOSS MUTATED`
TCGA-18-3408 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-4083 TCGA-18-4721 
       75.75        11.34        92.15        31.99         6.18       154.32 
TCGA-18-5592 TCGA-21-1076 TCGA-21-5783 TCGA-22-0940 TCGA-22-1012 TCGA-22-4595 
       49.94        60.89        88.11        21.99        14.10        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4609 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
        0.56        38.17         9.57        63.55        44.25         0.79 
TCGA-22-5479 TCGA-22-5483 TCGA-22-5492 TCGA-33-4547 TCGA-33-4583 TCGA-33-AASB 
       54.28        18.84        16.64        79.53       151.27         6.94 
TCGA-33-AASD TCGA-34-2596 TCGA-34-2604 TCGA-34-8455 TCGA-37-5819 TCGA-39-5016 
      110.99         2.63        31.50         4.04         3.39        74.07 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5034 TCGA-39-5037 TCGA-39-5039 TCGA-43-6143 
       68.58        60.79        36.39        35.70        17.88        12.36 
TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 
       13.38         2.93        11.61         9.73        12.03         9.99 
TCGA-46-6025 TCGA-51-4081 TCGA-52-7622 TCGA-56-7579 TCGA-56-7582 TCGA-56-8624 
       10.65        29.95        28.34         1.45         0.85         1.18 
TCGA-56-A4ZK TCGA-58-8386 TCGA-60-2698 TCGA-60-2707 TCGA-60-2722 TCGA-60-2726 
       18.74         0.03        10.22        21.93        29.85        11.77 
TCGA-63-A5MJ TCGA-63-A5MR TCGA-66-2758 TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 
       59.97        89.29        21.01        12.03        12.00        25.97 
TCGA-66-2789 TCGA-66-2792 TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I 
        4.04        30.02        54.08         2.73         6.64        16.18 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8140 TCGA-77-8150 
        6.51        53.95        37.81        12.59        11.54        54.41 
TCGA-77-A5G3 TCGA-77-A5G8 TCGA-85-7696 TCGA-85-7698 TCGA-85-7950 TCGA-85-8049 
      117.57        42.41        36.53        31.30        18.94        19.04 
TCGA-85-8070 TCGA-85-8277 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ 
       31.56        10.09        15.62        19.33        14.96        18.18 
TCGA-85-A4QR TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7767 TCGA-92-7341 TCGA-92-8064 
       19.73        15.85         3.65         2.93         3.48         5.26 
TCGA-92-8065 TCGA-94-A5I4 TCGA-96-7544 TCGA-96-A4JK TCGA-98-A53I TCGA-98-A53J 
        2.30        16.14        49.87        19.36        18.58        20.71 
TCGA-NC-A5HH TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5D1 
        1.22         2.89        37.22        14.73        83.57        16.80 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
       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-18-3411 TCGA-18-3414 
       12.20         7.46        79.46         4.80       117.57        23.54 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 
       36.07         1.64        86.96         2.79        27.19       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-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
      122.43         9.34       119.80        43.23        31.63        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       33.93        10.82        32.19         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
       64.21         1.74        27.02        48.82        20.48        35.08 
TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
       48.33        34.75        13.12        32.02        19.30        11.77 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
       31.73        64.93        14.63        71.34        79.20        11.74 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       30.12        62.86        56.32        22.06         7.63       133.74 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
       98.01       174.08       103.53        14.07        54.44         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASI 
       19.76        27.02         4.70         0.30        36.62        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
      118.36        27.16        61.61        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        67.79        56.38         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        30.94        18.15         4.96         1.12        27.19 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       26.43        20.91         3.95         0.43         0.39         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 
        8.12         7.46         7.82         6.81         0.39        47.80 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       44.75        55.20        70.03         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
       27.39        15.58        35.64        17.06        40.21        22.49 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
       38.66        27.02        33.11        18.38        27.91        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
       21.47         5.46         3.81        19.59         7.76        66.51 
TCGA-43-8116 TCGA-43-A56U TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 
       11.77        14.20        13.91         0.39         0.39         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         0.10        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 
        2.04         0.62         0.99         0.43         0.99         1.32 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 
        6.51         0.10        17.49         3.48        26.89        17.00 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 
       14.07         1.35        16.77         1.81        22.75        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-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 
       17.85        21.04         0.13         0.26         2.76        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-60-2696 
       34.36        56.65        35.24        29.92        21.11         3.58 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
       12.23        96.82        37.94        92.71        80.45        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       66.54        41.42         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
       48.49        42.64         3.19        32.32        35.90        23.57 
TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5ML 
       26.83       102.67        70.62        66.61        58.65        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       14.99        11.34        25.28        78.28        16.37        25.41 
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-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       43.99        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-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 
       19.00         3.98        24.95         1.97        40.01        22.98 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 
       22.98         5.03        10.06         4.01        49.05         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
        8.02        13.35        14.73        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       23.28        11.18        89.98        20.78         0.49        42.28 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
       70.13       106.95         0.16        46.78        15.75        86.76 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 
       82.92        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         9.63        65.49        35.90         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB 
      126.18       132.36        22.29         5.92        42.08        30.81 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
       27.62        38.86         9.67        11.97        12.99         6.41 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 
       34.95        32.91         1.38         1.15        29.95        25.15 
TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
       24.13        14.07        16.87        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-85-8664 
        0.72         7.76        14.63        13.94        12.59         0.10 
TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
       25.68        17.72        24.36        12.56        16.21        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 
        0.79        12.39        24.92         9.50        11.77        14.07 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-94-7033 
       20.22        22.62        10.59         2.70         4.01        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        0.16        11.70         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       17.69        57.07        18.31        17.46        16.57         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH 
       18.15         2.01        27.02        21.21        20.32        19.10 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
       12.89        16.11        13.18        13.41        11.84         0.07 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
       64.08         4.54        51.78        45.37        13.74         4.21 
TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CT 
       39.85        30.58        24.00        29.75        22.78        65.49 
TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52S TCGA-O2-A52W TCGA-O2-A5IB 
        3.65         0.43        12.72         8.58        11.18 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.03              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           154.32            174.08 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            18.66             19.76 
[1] "0.0 - 154.3 (18.7)" "0.1 - 174.1 (19.8)"
[1] "hr=" "1"  
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         1       16       34        1        18        24
  6P LOSS WILD-TYPE       1       71      117        1        45        68
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  6P LOSS MUTATED           1         13          2        2
  6P LOSS WILD-TYPE         2         49         19        5
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                16                71
  STAGE IB                34               117
  STAGE II                 1                 1
  STAGE IIA               18                45
  STAGE IIB               24                68
  STAGE III                1                 2
  STAGE IIIA              13                49
  STAGE IIIB               2                19
  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    23  66  20   3
  6P LOSS WILD-TYPE  88 224  49  20
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              23                88
  T2              66               224
  T3              20                49
  T4               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                 N0  N1  N2  N3
  6P LOSS MUTATED    64  38   7   1
  6P LOSS WILD-TYPE 248  93  32   4
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              64               248
  N1              38                93
  N2               7                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"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    94   2
  6P LOSS WILD-TYPE 310   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     94    2
  6P LOSS WILD-TYPE  310    5
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              94               310
  1               2                 5
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    25  87
  6P LOSS WILD-TYPE 102 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     25   87
  6P LOSS WILD-TYPE  102  279
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              25               102
  MALE                87               279
[1] 2 2
[1] FALSE
D52V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED                                       4
  6P LOSS WILD-TYPE                                    11
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED                                         0
  6P LOSS WILD-TYPE                                       1
                   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                                                           107
  6P LOSS WILD-TYPE                                                         363
D52V9, multiclass
                                                             clus
vv                                                            6P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG CLEAR CELL 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)             107
                                                             clus
vv                                                            6P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               363
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2 110
  6P LOSS WILD-TYPE  11 370
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2  110
  6P LOSS WILD-TYPE   11  370
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                2                11
  YES             110               370
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, continuous
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    91   2   0   8
  6P LOSS WILD-TYPE 303  10   4  14
D52V13, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              91               303
  R1               2                10
  R2               0                 4
  RX               8                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
  6P LOSS MUTATED       1                         6    77
  6P LOSS WILD-TYPE     8                        25   263
D52V14, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               6                25
  WHITE                                  77               263
[1] 3 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  70
  6P LOSS WILD-TYPE   6 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   70
  6P LOSS WILD-TYPE    6  239
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              70               239
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    63  45
  6Q LOSS WILD-TYPE 218 151
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              108               369 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               45               151 
$`6Q LOSS MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-4083 
       75.75       117.57        11.34        92.15        31.99         6.18 
TCGA-18-5592 TCGA-21-1076 TCGA-21-5783 TCGA-21-5787 TCGA-22-0940 TCGA-22-4595 
       49.94        60.89        88.11        10.82        21.99        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-5478 TCGA-22-5479 
        0.56        38.17        34.75        19.30         0.79        54.28 
TCGA-22-5492 TCGA-33-4582 TCGA-33-4583 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
       16.64       103.53       151.27         6.94       110.99        44.19 
TCGA-34-2596 TCGA-34-2604 TCGA-34-5928 TCGA-34-8455 TCGA-37-5819 TCGA-39-5016 
        2.63        31.50        18.15         4.04         3.39        74.07 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5034 TCGA-39-5037 TCGA-39-5039 TCGA-43-2581 
       68.58        60.79        36.39        35.70        17.88        38.66 
TCGA-43-6143 TCGA-43-8115 TCGA-43-8118 TCGA-46-6025 TCGA-51-4081 TCGA-52-7622 
       12.36        13.38         2.93        10.65        29.95        28.34 
TCGA-52-7812 TCGA-56-7582 TCGA-56-7730 TCGA-56-8624 TCGA-56-8625 TCGA-56-A4BY 
       27.45         0.85         6.51         1.18        10.36        17.85 
TCGA-56-A4ZK TCGA-58-8386 TCGA-58-A46M TCGA-60-2707 TCGA-60-2722 TCGA-60-2726 
       18.74         0.03        35.24        21.93        29.85        11.77 
TCGA-63-A5MR TCGA-66-2758 TCGA-66-2763 TCGA-66-2773 TCGA-66-2780 TCGA-66-2782 
       89.29        21.01         0.99         3.02        12.03        12.00 
TCGA-66-2783 TCGA-66-2792 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I 
       24.95        30.02         4.01         2.73         6.64        16.18 
TCGA-77-7141 TCGA-77-8007 TCGA-77-8009 TCGA-77-8131 TCGA-77-8140 TCGA-77-8150 
        0.49         6.51        53.95        12.59        11.54        54.41 
TCGA-77-A5G8 TCGA-85-6560 TCGA-85-7696 TCGA-85-7698 TCGA-85-7710 TCGA-85-8052 
       42.41        11.97        36.53        31.30         1.38        24.13 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8354 TCGA-85-8479 TCGA-85-A4JC 
       31.56        16.87        10.09        32.71         0.72        14.96 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A5B5 
       18.18        19.73        12.56        16.21        15.85         3.65 
TCGA-90-7767 TCGA-92-7341 TCGA-92-8065 TCGA-94-8491 TCGA-96-7544 TCGA-96-A4JK 
        2.93         3.48         2.30        26.63        49.87        19.36 
TCGA-98-A538 TCGA-98-A53I TCGA-J1-A4AH TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HN 
       27.16        18.58        19.10        51.78         1.22        37.22 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-XC-AA0X 
       14.73        29.75        16.80        33.07         3.72         0.20 

$`6Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3417 
       12.20         7.46        79.46         4.80        23.54        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
        1.64        86.96         2.79       154.32        27.19       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-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
      122.43         9.34       119.80        43.23        31.63        41.69 
TCGA-21-5786 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       33.93        32.19         7.33        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
        1.74        14.10        27.02        48.82        20.48        35.08 
TCGA-22-4594 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       48.33        13.12        32.02         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
       64.93        63.55        14.63        44.25        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 
       11.74        18.84        30.12        62.86        56.32        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 
        7.63       133.74        98.01        79.53       174.08        14.07 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       54.44         1.55        19.76        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 
       36.62       118.36        27.16        61.61        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.27        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       12.00        16.93        30.94         4.96         1.12        27.19 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       26.43        20.91         3.95         0.43         0.39         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 
        8.12         7.46         7.82         6.81         0.39        47.80 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       44.75        55.20        70.03         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
       27.39        15.58        35.64        17.06        40.21        22.49 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
       27.02        33.11        18.38        27.91        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 
        5.46         3.81        19.59         7.76        66.51        11.77 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 
       11.61         9.73        14.20        12.03         9.99        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
        0.39         0.39         5.46        30.35         8.75        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        0.10        18.25         2.04         0.62         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        0.99         1.45         1.32         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
       26.89        17.00        14.07         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
       22.75         9.93        20.25        15.81        20.94        19.23 
TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 
       13.32        21.04         0.13         0.26         2.76        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-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 
       34.36        56.65        29.92        21.11         3.58        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
       10.22        96.82        37.94        92.71        80.45        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       66.54        41.42         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
       48.49        42.64         3.19        32.32        35.90        23.57 
TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ 
       26.83       102.67        70.62        66.61        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT 
       45.57        14.99        11.34        25.28        78.28        16.37 
TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       25.41        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-66-2759 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-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 
        2.01         7.07        23.01        19.00         2.01        19.00 
TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
        3.98         1.97        25.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7757 
       22.98         5.03        10.06        54.08        49.05         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
        8.02        13.35        14.73        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7142 TCGA-77-7335 
       23.28        11.18        89.98        20.78        42.28        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        15.75        86.76        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 
       82.92        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         9.63        65.49        35.90         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA 
      126.18       132.36       117.57        22.29         5.92        42.08 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 
       30.81        27.62        38.86         9.67        12.99         6.41 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       34.95        32.91         1.15        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       19.04        14.07        34.52         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
       16.77         5.29         3.09         2.01         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       13.94        12.59         0.10        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       17.72        24.36        14.96         0.79        12.39        24.92 
TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        9.50        11.77        14.07        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        2.70         4.01         5.26        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 
        4.01         5.03        14.14        16.14        17.69        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 
       18.31        17.46        16.57         8.42         2.76        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.67        21.34         3.88        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       21.21        20.32        20.71        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HI 
       13.41        11.84         0.07        64.08         4.54        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21         2.89        39.85        30.58        24.00 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52S 
       22.78        83.57        65.49         3.65         0.43        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       43.89         8.58        11.18 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.03              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           151.27            174.08 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            18.38             19.59 
[1] "0.0 - 151.3 (18.4)" "0.1 - 174.1 (19.6)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         1       15       33        0        21        24
  6Q LOSS WILD-TYPE       1       72      118        2        42        68
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  6Q LOSS MUTATED           1         14          2        2
  6Q LOSS WILD-TYPE         2         48         19        5
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                15                72
  STAGE IB                33               118
  STAGE II                 0                 2
  STAGE IIA               21                42
  STAGE IIB               24                68
  STAGE III                1                 2
  STAGE IIIA              14                48
  STAGE IIIB               2                19
  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    20  71  18   4
  6Q LOSS WILD-TYPE  91 219  51  19
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              20                91
  T2              71               219
  T3              18                51
  T4               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                 N0  N1  N2  N3
  6Q LOSS MUTATED    65  37   8   1
  6Q LOSS WILD-TYPE 247  94  31   4
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              65               247
  N1              37                94
  N2               8                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"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    94   2
  6Q LOSS WILD-TYPE 310   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     94    2
  6Q LOSS WILD-TYPE  310    5
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              94               310
  1               2                 5
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    30  83
  6Q LOSS WILD-TYPE  97 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     30   83
  6Q LOSS WILD-TYPE   97  283
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              30                97
  MALE                83               283
[1] 2 2
[1] FALSE
D53V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED                                       6
  6Q LOSS WILD-TYPE                                     9
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED                                         0
  6Q LOSS WILD-TYPE                                       1
                   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                                                           105
  6Q LOSS WILD-TYPE                                                         365
D53V9, multiclass
                                                             clus
vv                                                            6Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             105
                                                             clus
vv                                                            6Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               365
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3 110
  6Q LOSS WILD-TYPE  10 370
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  110
  6Q LOSS WILD-TYPE   10  370
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                3                10
  YES             110               370
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    91   2   1   8
  6Q LOSS WILD-TYPE 303  10   3  14
D53V13, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              91               303
  R1               2                10
  R2               1                 3
  RX               8                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
  6Q LOSS MUTATED       2                         7    79
  6Q LOSS WILD-TYPE     7                        24   261
D53V14, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               7                24
  WHITE                                  79               261
[1] 3 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  71
  6Q LOSS WILD-TYPE   5 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   71
  6Q LOSS WILD-TYPE    5  238
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              71               238
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    33  23
  7P LOSS WILD-TYPE 248 173
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               56               421 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               23               173 
$`7P LOSS MUTATED`
TCGA-18-3419 TCGA-21-1077 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
        1.64        34.78        43.23        33.93        10.82        32.19 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4601 TCGA-22-5492 TCGA-33-6738 TCGA-33-AASJ 
       27.02        48.82        34.75        16.64        27.02       118.36 
TCGA-37-3789 TCGA-37-4133 TCGA-37-5819 TCGA-39-5029 TCGA-39-5036 TCGA-43-2578 
        0.43         7.82         3.39        24.33        35.64        22.49 
TCGA-43-6770 TCGA-46-6026 TCGA-56-1622 TCGA-56-5898 TCGA-56-6546 TCGA-56-7580 
       21.47        13.91        28.96        18.25         0.62         1.32 
TCGA-56-8629 TCGA-58-8386 TCGA-58-8390 TCGA-60-2695 TCGA-60-2703 TCGA-63-A5MS 
       15.81         0.03        29.95        21.11        96.82        78.28 
TCGA-66-2757 TCGA-66-2773 TCGA-66-2783 TCGA-66-2788 TCGA-66-2792 TCGA-66-2793 
       43.99         3.02        24.95        22.98        30.02        10.06 
TCGA-77-7142 TCGA-77-7337 TCGA-77-8143 TCGA-77-8144 TCGA-77-A5GH TCGA-85-6560 
       42.28       106.95        26.40        27.39        38.86        11.97 
TCGA-85-7699 TCGA-85-8070 TCGA-85-8277 TCGA-85-8353 TCGA-85-A4JB TCGA-85-A510 
       32.91        31.56        10.09         3.09        17.72        15.85 
TCGA-90-7767 TCGA-94-A5I4 TCGA-98-A538 TCGA-J1-A4AH TCGA-NC-A5HK TCGA-NC-A5HO 
        2.93        16.14        27.16        19.10         4.21        30.58 
TCGA-NC-A5HT TCGA-O2-A5IB 
       22.78        11.18 

$`7P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 
       11.34        23.54        92.15        31.99        36.07        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
        6.18         2.79       154.32        49.94        27.19       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
       46.88        99.16        70.16        60.89        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-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       21.99         7.33        14.93         4.31        64.21         1.74 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       14.10        20.48        35.08        48.33        24.13         0.56 
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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       31.73        64.93        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 
       54.28        71.34        79.20        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
       62.86        56.32        22.06         7.63       133.74        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       79.53       174.08       103.53       151.27        14.07        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
        1.55        19.76         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
      110.99        44.19        27.16         2.63        61.61        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       28.96        32.88        31.27        65.23        67.79        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        23.24        12.00        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
        4.96         1.12        27.19         4.04        26.43        20.91 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
        3.95         0.39         6.58         8.12         7.46         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        0.39        47.80        74.07        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       70.03        60.79         1.71         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
       15.58        35.70        17.88        17.06        40.21        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       27.02        33.11        18.38        27.91        12.36        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
        5.46         3.81        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
       11.77         2.93        11.61         9.73        14.20        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        9.99        10.65         0.39         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 
        5.46        30.35         8.75        27.45         0.10         2.04 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
        0.99         0.43         0.99         1.45         0.85         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.10        17.49         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
        9.93        20.25        20.94        19.23        13.32        17.85 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 
       21.04        18.74         0.13         0.26         2.76        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-60-2696 TCGA-60-2697 TCGA-60-2698 
       56.65        35.24        29.92         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       41.42         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       42.64         3.19        32.32        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       26.83        11.77       102.67        70.62        66.61        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-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       16.37        25.41        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-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.92         0.99        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-66-2785 
        2.01        19.00        12.03         3.98        12.00         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 
       25.97        40.01         4.04        22.98         5.03        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
        4.01        49.05         2.73         6.64         6.94         8.02 
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-77-7140 TCGA-77-7141 TCGA-77-7335 
       23.28        11.18        89.98        20.78         0.49        70.13 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        0.16        46.78        15.75         6.51        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       37.81        82.92        12.59        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
      104.09        11.54         6.97         9.63        54.41        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
       35.90         0.33       126.18       132.36       117.57        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6175 
        5.92        42.41        42.08        30.81        27.62         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
       12.99         6.41        36.53        34.95        31.30         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-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       14.07        16.87        34.52         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         5.29        32.71         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       19.33        14.96        24.36        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       16.21        14.96         0.79        12.39         3.65        24.92 
TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        9.50        11.77        14.07        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
        2.70         3.48         4.01         5.26         2.30        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        0.16        11.70         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       17.69        49.87        57.07        18.31        17.46        19.36 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       16.57         8.42         2.76        30.81        30.67        21.34 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        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-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       11.84         0.07        64.08         4.54        51.78         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP 
       45.37        13.74         2.89        39.85        37.22        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       14.73        29.75        83.57        65.49         3.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
        0.43        33.07         3.72        12.72        43.89         8.58 
TCGA-XC-AA0X 
        0.20 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.03              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           118.36            174.08 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            22.88             18.84 
[1] "0.0 - 118.4 (22.9)" "0.1 - 174.1 (18.8)"
[1] "hr=" "1"  
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0        6       16        0         7        11
  7P LOSS WILD-TYPE       2       81      135        2        56        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  7P LOSS MUTATED           1         12          3        1
  7P LOSS WILD-TYPE         2         50         18        6
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 6                81
  STAGE IB                16               135
  STAGE II                 0                 2
  STAGE IIA                7                56
  STAGE IIB               11                81
  STAGE III                1                 2
  STAGE IIIA              12                50
  STAGE IIIB               3                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
  7P LOSS MUTATED    10  34   9   4
  7P LOSS WILD-TYPE 101 256  60  19
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1              10               101
  T2              34               256
  T3               9                60
  T4               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                 N0  N1  N2  N3
  7P LOSS MUTATED    32  17   6   1
  7P LOSS WILD-TYPE 280 114  33   4
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              32               280
  N1              17               114
  N2               6                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"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    46   1
  7P LOSS WILD-TYPE 358   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     46    1
  7P LOSS WILD-TYPE  358    6
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              46               358
  1               1                 6
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    11  46
  7P LOSS WILD-TYPE 116 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     11   46
  7P LOSS WILD-TYPE  116  320
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE              11               116
  MALE                46               320
[1] 2 2
[1] FALSE
D54V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                       1
  7P LOSS WILD-TYPE                                    14
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                         0
  7P LOSS WILD-TYPE                                       1
                   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                                                            56
  7P LOSS WILD-TYPE                                                         414
D54V9, multiclass
                                                             clus
vv                                                            7P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG CLEAR CELL 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)              56
                                                             clus
vv                                                            7P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               414
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2  55
  7P LOSS WILD-TYPE  11 425
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   55
  7P LOSS WILD-TYPE   11  425
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                2                11
  YES              55               425
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, continuous
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    49   0   2   2
  7P LOSS WILD-TYPE 345  12   2  20
D54V13, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              49               345
  R1               0                12
  R2               2                 2
  RX               2                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
  7P LOSS MUTATED       0                         3    41
  7P LOSS WILD-TYPE     9                        28   299
D54V14, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               3                28
  WHITE                                  41               299
[1] 3 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  35
  7P LOSS WILD-TYPE   7 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   35
  7P LOSS WILD-TYPE    7  274
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              35               274
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    30  19
  7Q LOSS WILD-TYPE 251 177
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               49               428 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               19               177 
$`7Q LOSS MUTATED`
TCGA-18-3419 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-22-1016 TCGA-22-1017 
        1.64       119.80        43.23        33.93        27.02        48.82 
TCGA-22-5481 TCGA-37-3789 TCGA-37-5819 TCGA-39-5029 TCGA-43-2578 TCGA-43-2581 
       79.20         0.43         3.39        24.33        22.49        38.66 
TCGA-43-6770 TCGA-43-6771 TCGA-46-6026 TCGA-56-1622 TCGA-56-6546 TCGA-56-7580 
       21.47         5.46        13.91        28.96         0.62         1.32 
TCGA-56-8629 TCGA-56-A4BW TCGA-60-2695 TCGA-60-2703 TCGA-63-A5MH TCGA-63-A5MS 
       15.81        19.23        21.11        96.82        66.61        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-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 
      104.09        27.39        30.81        38.86        11.97        32.91 
TCGA-85-8048 TCGA-85-8353 TCGA-85-A4JB TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L 
       25.15         3.09        17.72        15.85         0.79        12.39 
TCGA-90-7767 TCGA-94-A5I4 TCGA-98-8022 TCGA-J1-A4AH TCGA-NC-A5HK TCGA-NC-A5HM 
        2.93        16.14        30.67        19.10         4.21        39.85 
TCGA-O2-A52N 
       33.07 

$`7Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 
       11.34        23.54        92.15        31.99        36.07        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
        6.18         2.79       154.32        49.94        27.19       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-21-5782 TCGA-21-5783 TCGA-21-5784 
       31.73       122.43         9.34        31.63        88.11        41.69 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       10.82        32.19        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
       64.21         1.74        14.10        20.48        35.08        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-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 
       14.63        44.25         0.79        54.28        71.34        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       18.84        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
        7.63       133.74        98.01        79.53       174.08       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      151.27        14.07        54.44         1.55        19.76        27.02 
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-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       32.88        31.27        65.23        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       23.24        12.00        16.93        30.94        18.15         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        27.19         4.04        26.43        20.91         3.95 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.39         6.58         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        0.39        47.80        74.07        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       70.03        60.79         1.71         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
       15.58        35.64        35.70        17.88        17.06        40.21 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       27.02        33.11        18.38        27.91        12.36        24.89 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        3.81        19.59         7.76        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
        2.93        11.61         9.73        14.20        12.03         9.99 
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         0.10        18.25         2.04 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
        0.99         0.43         0.99         1.45         0.85         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.10        17.49         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
        9.93        20.25        20.94        13.32        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       18.74         0.13         0.26         2.76         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-60-2696 TCGA-60-2697 
       34.36        56.65        35.24        29.92         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       66.54        41.42         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
       48.49        42.64         3.19        32.32        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       23.57        26.83        11.77       102.67        70.62        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-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       16.37        25.41        36.16        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 
       43.10         2.01        21.07         0.99         1.02         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-66-2789 TCGA-66-2790 TCGA-66-2791 
        1.97        25.97        40.01         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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
        6.94         8.02        13.35        16.18        14.73        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       73.12        75.09        23.28        89.98        20.78         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       42.28        70.13       106.95         0.16        46.78        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        6.51        86.76        53.95        37.81        82.92        12.59 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
       53.92        17.72        11.54        26.40         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       54.41        65.49        35.90         0.33       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
      117.57        22.29         5.92        42.41        42.08        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
        9.67        12.99         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        14.07        16.87        34.52        10.09         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 
        0.72         7.76        14.63        13.94        12.59         0.10 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       15.62        25.68        19.33        14.96        24.36        18.18 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A5B5 TCGA-90-6837 
       19.73        12.56        16.21        14.96         3.65        24.92 
TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        9.50        11.77        14.07        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
        2.70         3.48         4.01         5.26         2.30        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        0.16        11.70         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       17.69        49.87        57.07        18.31        17.46        19.36 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 
       16.57         8.42         2.76        30.81        21.34        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        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-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       11.84         0.07        64.08         4.54        51.78         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       45.37        13.74         2.89        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       14.73        29.75        22.78        83.57        65.49         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
       16.80         0.43         3.72        12.72        43.89         8.58 
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            174.08 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            21.47             18.97 
[1] "0.4 - 119.8 (21.5)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         1        8       17        0         7        10
  7Q LOSS WILD-TYPE       1       79      134        2        56        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  7Q LOSS MUTATED           0          6          1        0
  7Q LOSS WILD-TYPE         3         56         20        7
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 8                79
  STAGE IB                17               134
  STAGE II                 0                 2
  STAGE IIA                7                56
  STAGE IIB               10                82
  STAGE III                0                 3
  STAGE IIIA               6                56
  STAGE IIIB               1                20
  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    10  33   5   2
  7Q LOSS WILD-TYPE 101 257  64  21
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              10               101
  T2              33               257
  T3               5                64
  T4               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                 N0  N1  N2  N3
  7Q LOSS MUTATED    32  13   3   0
  7Q LOSS WILD-TYPE 280 118  36   5
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              32               280
  N1              13               118
  N2               3                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"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    41   0
  7Q LOSS WILD-TYPE 363   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     41    0
  7Q LOSS WILD-TYPE  363    7
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              41               363
  1               0                 7
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    10  40
  7Q LOSS WILD-TYPE 117 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     10   40
  7Q LOSS WILD-TYPE  117  326
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              10               117
  MALE                40               326
[1] 2 2
[1] FALSE
D55V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                       1
  7Q LOSS WILD-TYPE                                    14
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                         0
  7Q LOSS WILD-TYPE                                       1
                   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                                                         421
D55V9, multiclass
                                                             clus
vv                                                            7Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG CLEAR CELL 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                                                            7Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               421
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  49
  7Q LOSS WILD-TYPE  12 431
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   49
  7Q LOSS WILD-TYPE   12  431
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                12
  YES              49               431
[1] 2 2
[1] FALSE
D55V11, continuous
D55V12, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    44   0   1   3
  7Q LOSS WILD-TYPE 350  12   3  19
D55V13, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              44               350
  R1               0                12
  R2               1                 3
  RX               3                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       2                         1    34
  7Q LOSS WILD-TYPE     7                        30   306
D55V14, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               1                30
  WHITE                                  34               306
[1] 3 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  32
  7Q LOSS WILD-TYPE   7 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   32
  7Q LOSS WILD-TYPE    7  277
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              32               277
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   133  98
  8P LOSS WILD-TYPE 148  98
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              231               246 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               98                98 
$`8P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3412 TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-4721 
       12.20        11.34        92.15         1.64         6.18       154.32 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 
       49.94        27.19        99.16        60.89       122.43        43.23 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-1000 TCGA-22-1002 TCGA-22-1016 
       31.63        33.93        10.82        14.93         4.31        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       48.82        20.48        48.33        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5477 TCGA-22-5478 
       32.02         9.57        11.77        31.73        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-33-4589 TCGA-33-6738 
       79.53       174.08       103.53        14.07         1.55        27.02 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL 
        4.70         0.30        36.62       110.99        44.19        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2609 TCGA-34-5236 TCGA-34-5241 TCGA-34-5928 
        2.63        61.61        31.27         9.07        16.93        18.15 
TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4135 
       27.19         4.04         3.95         0.43         0.39         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 TCGA-39-5037 
        0.39        47.80        68.58        60.79        27.39        35.70 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-5668 TCGA-43-6770 TCGA-43-6771 
       17.88        40.21        38.66        18.38        21.47         5.46 
TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-46-3768 
        7.76        13.38        11.77         2.93        11.61         9.99 
TCGA-46-6025 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
       10.65         0.39        29.95        28.34         5.46        30.35 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 
       27.45        28.96         0.10        18.25         0.43         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-8504 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
        1.45         1.32        16.77         9.93        20.25        15.81 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8390 TCGA-58-8392 
       19.23        13.32        17.85         0.26        29.95        16.47 
TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2698 TCGA-60-2703 
       34.78        34.36        56.65        35.24        10.22        96.82 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2721 TCGA-60-2723 TCGA-60-2726 TCGA-63-A5MJ 
       41.42        56.91        32.32        35.90        11.77        59.97 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       14.99        11.34        25.28        78.28        16.37        25.41 
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-66-2769 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
        7.07        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7755 
       40.01        22.98         5.03        30.02         4.01         2.73 
TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 
        8.02        16.18        14.73        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        15.75        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
       37.81        82.92       104.09        11.54        27.39         6.97 
TCGA-77-8148 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA 
        9.63        35.90       117.57        22.29        42.41        42.08 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       27.62         9.67        12.99         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-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 
       31.56        34.52        10.09        22.45         5.29         3.09 
TCGA-85-8354 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
       32.71        19.33        17.72        14.96        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 
       12.56        16.21        14.96        12.39         3.65         9.50 
TCGA-90-7767 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-94-7557 TCGA-94-8491 
        2.93        20.22         3.48         4.01         0.16        26.63 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JK 
       14.14        16.14        17.69        49.87        17.46        19.36 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53J 
        2.76        30.81        30.67        27.16         3.88        20.71 
TCGA-J1-A4AH TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
       19.10        13.18        11.84        64.08        51.78        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT 
       13.74         2.89        24.00        14.73        29.75        22.78 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
        3.72        12.72        43.89 

$`8P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
        7.46        75.75        79.46         4.80       117.57        23.54 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-21-1070 TCGA-21-1071 
       31.99        36.07        86.96         2.79       119.54        46.88 
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-21-5783 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 
       88.11        41.69        32.19        21.99         7.33        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4607 
        1.74        14.10        35.08        24.13         0.56        19.30 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5489 
       64.93        63.55        14.63        54.28        11.74        62.86 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4583 TCGA-33-4587 
       22.06         7.63       133.74        98.01       151.27        54.44 
TCGA-33-6737 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       19.76         6.94       118.36        31.50        28.96        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
       65.23        67.79        56.38        23.24        12.00        30.94 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4129 TCGA-37-4130 
        4.96         1.12        26.43        20.91         6.58         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 
        7.46         7.82         3.39        74.07        44.75        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
       70.03         1.71        24.33         1.94        36.39        15.58 
TCGA-39-5036 TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       35.64        17.06        22.49        27.02        33.11        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-A475 
       12.36        24.89         3.81        19.59        66.51         9.73 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-52-7811 TCGA-56-6545 
       14.20        12.03        13.91         0.39         8.75         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
        0.62         0.99         0.85         6.51         0.10        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        3.48        26.89        17.00        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A4ZK 
       22.75         1.18        10.36        20.94        21.04        18.74 
TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 
        0.13         2.76         0.03        13.25        13.55        71.24 
TCGA-58-A46J TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2704 
       85.12        29.92        21.11         3.58        12.23        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
       92.71        21.93        80.45        49.48        66.54         9.01 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       50.33        35.34        48.49        42.64         3.19        29.85 
TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       23.57        26.83       102.67        70.62        66.61        58.65 
TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MY TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 
       45.57        89.29        34.59        21.07         0.99         0.99 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 
       21.01         0.99         2.01         2.01        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 
        3.02         2.01        19.00        25.97        22.98         4.04 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
       10.06        54.08        49.05         6.64         6.94        13.35 
TCGA-77-6843 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       73.12        89.98        20.78         0.49        42.28        70.13 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       46.78         6.51        12.59        53.92        39.09        17.72 
TCGA-77-8143 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       26.40        54.41        65.49         0.33       126.18       132.36 
TCGA-77-A5G7 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-8049 
        5.92        30.81        38.86        11.97        32.91        19.04 
TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
       24.13        14.07        16.87         0.76        13.22        16.77 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01         0.72         7.76        14.63        13.94        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A510 TCGA-85-A513 
        0.10        15.62        25.68        24.36        15.85         0.79 
TCGA-90-6837 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       24.92        11.77        14.07        22.62        10.59         2.70 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        5.26         2.30        21.04        11.70         4.01         5.03 
TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A53A 
       57.07        18.31        16.57         8.42        21.34        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
        2.01        27.02        21.21        20.32        18.58        12.89 
TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HK 
       16.11        13.41         0.07         4.54         1.22         4.21 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       39.85        37.22        30.58        83.57        65.49         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       16.80         0.43        33.07         8.58        11.18         0.20 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.10              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           174.08            151.27 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           18.940            19.445 
[1] "0.1 - 174.1 (18.9)" "0.0 - 151.3 (19.4)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         0       44       65        1        32        50
  8P LOSS WILD-TYPE       2       43       86        1        31        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  8P LOSS MUTATED           2         35          7        2
  8P LOSS WILD-TYPE         1         27         14        5
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                44                43
  STAGE IB                65                86
  STAGE II                 1                 1
  STAGE IIA               32                31
  STAGE IIB               50                42
  STAGE III                2                 1
  STAGE IIIA              35                27
  STAGE IIIB               7                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
  8P LOSS MUTATED    52 141  38   8
  8P LOSS WILD-TYPE  59 149  31  15
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              52                59
  T2             141               149
  T3              38                31
  T4               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                 N0  N1  N2  N3
  8P LOSS MUTATED   145  70  21   2
  8P LOSS WILD-TYPE 167  61  18   3
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0             145               167
  N1              70                61
  N2              21                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   198   2
  8P LOSS WILD-TYPE 206   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    198    2
  8P LOSS WILD-TYPE  206    5
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             198               206
  1               2                 5
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    58 181
  8P LOSS WILD-TYPE  69 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     58  181
  8P LOSS WILD-TYPE   69  185
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              58                69
  MALE               181               185
[1] 2 2
[1] FALSE
D56V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                       6
  8P LOSS WILD-TYPE                                     9
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                         1
  8P LOSS WILD-TYPE                                       0
                   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                                                           231
  8P LOSS WILD-TYPE                                                         239
D56V9, multiclass
                                                             clus
vv                                                            8P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             231
                                                             clus
vv                                                            8P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               239
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     7 232
  8P LOSS WILD-TYPE   6 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7  232
  8P LOSS WILD-TYPE    6  248
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                7                 6
  YES             232               248
[1] 2 2
[1] FALSE
D56V11, continuous
D56V12, continuous
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   192   6   2  12
  8P LOSS WILD-TYPE 202   6   2  10
D56V13, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             192               202
  R1               6                 6
  R2               2                 2
  RX              12                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                        14   164
  8P LOSS WILD-TYPE     5                        17   176
D56V14, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              14                17
  WHITE                                 164               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     3 146
  8P LOSS WILD-TYPE   5 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3  146
  8P LOSS WILD-TYPE    5  163
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO             146               163
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    29  17
  8Q LOSS WILD-TYPE 252 179
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               46               431 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               17               179 
$`8Q LOSS MUTATED`
TCGA-21-1072 TCGA-22-5483 TCGA-33-4586 TCGA-33-6738 TCGA-37-3792 TCGA-37-4135 
       99.16        18.84        14.07        27.02         0.39         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5037 TCGA-43-6771 TCGA-46-6025 TCGA-52-7622 
        0.39        47.80        35.70         5.46        10.65        28.34 
TCGA-52-7809 TCGA-56-7730 TCGA-56-8629 TCGA-56-A4BW TCGA-58-A46K TCGA-63-A5MP 
        5.46         6.51        15.81        19.23        34.36        25.28 
TCGA-63-A5MS TCGA-63-A5MU TCGA-66-2727 TCGA-66-2766 TCGA-66-2791 TCGA-77-8144 
       78.28        25.41        16.96         1.02         5.03        27.39 
TCGA-77-8154 TCGA-77-A5GF TCGA-85-6561 TCGA-85-7844 TCGA-85-8276 TCGA-85-8277 
       35.90        27.62        12.99        29.95        34.52        10.09 
TCGA-85-8352 TCGA-85-A4CN TCGA-85-A50M TCGA-85-A53L TCGA-90-7766 TCGA-90-A4ED 
        5.29        19.33        12.56        12.39         9.50        20.22 
TCGA-94-8491 TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI TCGA-NC-A5HJ 
       26.63        20.71        11.84        64.08        45.37        13.74 
TCGA-NC-A5HL TCGA-NC-A5HP TCGA-O2-A52S TCGA-O2-A52V 
        2.89        24.00        12.72        43.89 

$`8Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       11.34        23.54        92.15        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
       86.96         6.18         2.79       154.32        49.94        27.19 
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-21-1081 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-21-A5DI TCGA-22-0940 
       88.11        41.69        33.93        10.82        32.19        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
        7.33        14.93         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
       27.02        48.82        20.48        35.08        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
        0.56        38.17        34.75        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
        9.57        11.77        31.73        64.93        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        54.28        71.34        79.20        11.74 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
       30.12        62.86        56.32        16.64        22.06         7.63 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
      133.74        98.01        79.53       174.08       103.53       151.27 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       54.44         1.55        19.76         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-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
       61.61        31.50        28.96        32.88        31.27        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       67.79        56.38         9.07        23.24        12.00        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       30.94        18.15         4.96         1.12        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
       26.43        20.91         3.95         0.43         6.58         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        7.46         7.82         3.39        74.07        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        70.03        60.79         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 
       27.39        36.39        15.58        35.64        17.88        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       40.21        22.49        38.66        27.02        33.11        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 
       27.91        12.36        24.89        21.47         3.81        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        7.76        66.51        13.38        11.77         2.93        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 
        9.73        14.20        12.03         9.99        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
        0.39        29.95        30.35         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        0.10        18.25         2.04         0.62         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
        0.99         1.45         1.32         0.85         0.10        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
        3.48        26.89        17.00        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75         1.18        10.36         9.93        20.25 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       20.94        13.32        17.85        21.04        18.74         0.13 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26         2.76         0.03        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
       71.24        16.47        34.78        85.12        56.65        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       41.42         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       42.64         3.19        32.32        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       26.83        11.77       102.67        70.62        66.61        58.65 
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-66-2753 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-66-2767 TCGA-66-2768 
       21.01        25.05         0.99         2.01         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-66-2792 TCGA-66-2793 
       40.01        22.98         4.04        22.98        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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
        8.02        13.35        16.18        14.73        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       75.09        23.28        11.18        89.98        20.78         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       42.28        70.13       106.95         0.16        46.78        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        6.51        86.76        53.95        37.81        82.92        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-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ 
        6.97         9.63        54.41        65.49         0.33       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
      132.36       117.57        22.29         5.92        42.41        42.08 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
       30.81        38.86         9.67        11.97         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-85-8070 TCGA-85-8071 TCGA-85-8072 
       25.15        19.04        24.13        31.56        14.07        16.87 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
        0.76        13.22        22.45        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         0.72         7.76        14.63        13.94        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
        0.10        15.62        25.68        17.72        14.96        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       18.18        19.73        16.21        15.85        14.96         0.79 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
        3.65        24.92         2.93        11.77        14.07        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-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ 
       21.04         0.16        11.70         4.01         5.03        14.14 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
       16.14        17.69        49.87        57.07        18.31        17.46 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       19.36        16.57         8.42         2.76        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       21.34        27.16         3.88        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
       21.21        20.32        18.58        19.10        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       13.18        13.41         0.07         4.54        51.78         1.22 
TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HR 
        4.21        39.85        37.22        30.58        14.73        29.75 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE 
       22.78        83.57        65.49         3.65        16.80         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         3.72         8.58        11.18         0.20 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.39              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            99.16            174.08 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           19.035            19.100 
[1] "0.4 - 99.2 (19.0)"  "0.0 - 174.1 (19.1)"
[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       13        1        11         7
  8Q LOSS WILD-TYPE       2       82      138        1        52        85
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  8Q LOSS MUTATED           1          6          2        1
  8Q LOSS WILD-TYPE         2         56         19        6
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 5                82
  STAGE IB                13               138
  STAGE II                 1                 1
  STAGE IIA               11                52
  STAGE IIB                7                85
  STAGE III                1                 2
  STAGE IIIA               6                56
  STAGE IIIB               2                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
  8Q LOSS MUTATED     9  33   4   1
  8Q LOSS WILD-TYPE 102 257  65  22
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               9               102
  T2              33               257
  T3               4                65
  T4               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                 N0  N1  N2  N3
  8Q LOSS MUTATED    26  14   5   1
  8Q LOSS WILD-TYPE 286 117  34   4
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              26               286
  N1              14               117
  N2               5                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"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    38   1
  8Q LOSS WILD-TYPE 366   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     38    1
  8Q LOSS WILD-TYPE  366    6
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              38               366
  1               1                 6
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     9  38
  8Q LOSS WILD-TYPE 118 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9   38
  8Q LOSS WILD-TYPE  118  328
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               9               118
  MALE                38               328
[1] 2 2
[1] FALSE
D57V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED                                       2
  8Q LOSS WILD-TYPE                                    13
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED                                         0
  8Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  8Q LOSS MUTATED                                        0
  8Q LOSS WILD-TYPE                                      6
                   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                                                            45
  8Q LOSS WILD-TYPE                                                         425
D57V9, multiclass
                                                             clus
vv                                                            8Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG CLEAR CELL 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)              45
                                                             clus
vv                                                            8Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               425
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  46
  8Q LOSS WILD-TYPE  12 434
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   46
  8Q LOSS WILD-TYPE   12  434
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                1                12
  YES              46               434
[1] 2 2
[1] FALSE
D57V11, continuous
D57V12, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    37   2   0   1
  8Q LOSS WILD-TYPE 357  10   4  21
D57V13, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              37               357
  R1               2                10
  R2               0                 4
  RX               1                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
  8Q LOSS MUTATED       2                         1    34
  8Q LOSS WILD-TYPE     7                        30   306
D57V14, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               1                30
  WHITE                                  34               306
[1] 3 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  26
  8Q LOSS WILD-TYPE   7 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   26
  8Q LOSS WILD-TYPE    7  283
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              26               283
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   177 116
  9P LOSS WILD-TYPE 104  80
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              293               184 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              116                80 
$`9P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       12.20        79.46       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 
       36.07         1.64         6.18         2.79        49.94       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 
       46.88        99.16        70.16        34.78       122.43       119.80 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1002 
       43.23        88.11        33.93        10.82        32.19         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-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       48.33        38.17        34.75        19.30         9.57        11.77 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 
       31.73        64.93        14.63        44.25         0.79        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4547 
       18.84        30.12        56.32        22.06        98.01        79.53 
TCGA-33-4582 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB 
      103.53        19.76        27.02         4.70        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
      110.99        44.19        27.16         2.63        61.61        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 
       28.96        32.88        31.27        65.23        67.79        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       30.94         4.96        27.19         4.04        26.43        20.91 
TCGA-37-3789 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 
        0.43         8.12         6.81         0.39        47.80        74.07 
TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5035 
       44.75        60.79         1.71        24.33        27.39        15.58 
TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       17.06        40.21        27.02        33.11        18.38        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 
       24.89        21.47         5.46        19.59         7.76        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 
       11.77         2.93        11.61        12.03         9.99        13.91 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       29.95         5.46        30.35        28.96         0.10        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
        2.04         0.62         0.99         0.43         0.99         1.45 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        1.32         0.85         6.51         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
       26.89        14.07         1.35         1.81         1.18        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-A4ZJ TCGA-56-A5DS TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
       21.04         0.26        13.25        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 
       34.78        85.12        56.65         3.58        10.22        96.82 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2719 TCGA-60-2720 
       92.71        21.93        80.45        41.42        42.64         3.19 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG 
       32.32        35.90        23.57        26.83        11.77        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW 
       66.61        58.65        89.29        78.28        16.37        53.88 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 
       16.96        43.10         2.01        21.07         1.02         0.92 
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-66-2773 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-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 
        1.97        25.97        22.98         4.04        22.98        10.06 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
        6.94        13.35        16.18        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        42.28        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 
       15.75        86.76        53.95        37.81        82.92        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         9.63        65.49 
TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH 
       35.90       132.36        22.29         5.92        42.41        38.86 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       11.97        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         0.72        14.63         0.10        15.62 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50M 
       25.68        19.33        17.72        14.96        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96         0.79        12.39         3.65 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        9.50         2.93        14.07        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        3.48         4.01         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
        4.01        14.14        17.69        57.07        18.31        17.46 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       19.36        16.57         2.76        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J TCGA-L3-A524 
       27.16         3.88        18.15         2.01        20.71        16.11 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HO 
       13.41        11.84         0.07        51.78        45.37        30.58 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       24.00        14.73        22.78        83.57        65.49         3.65 
TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
       16.80         3.72        12.72        43.89         8.58 

$`9P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3416 TCGA-18-3421 TCGA-18-4721 
        7.46        75.75         4.80        31.99        86.96       154.32 
TCGA-18-5595 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5782 
       27.19        60.89        15.58        31.73         9.34        31.63 
TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1017 TCGA-22-4595 
       41.69        21.99         7.33        14.93        48.82        24.13 
TCGA-22-4596 TCGA-22-4604 TCGA-22-4605 TCGA-22-5473 TCGA-22-5479 TCGA-22-5480 
        0.56        13.12        32.02        63.55        54.28        71.34 
TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 
       79.20        62.86        16.64         7.63       133.74       174.08 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-A5GW TCGA-33-AASJ 
      151.27        14.07        54.44         1.55         0.30       118.36 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 
       56.38         9.07        23.24        12.00        18.15         1.12 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 
        3.95         0.39         6.58         7.46         7.82         3.39 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5030 TCGA-39-5034 TCGA-39-5036 
       68.58        55.20        70.03         1.94        36.39        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 TCGA-43-2581 TCGA-43-6143 TCGA-43-6773 
       35.70        17.88        22.49        38.66        12.36         3.81 
TCGA-43-7658 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
       66.51         9.73        14.20        10.65         0.39         0.39 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-8308 TCGA-56-8504 TCGA-56-8623 
       28.34         8.75        27.45        17.00        16.77        22.75 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 
       17.85        18.74         0.13         2.76         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-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       49.48        66.54         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2722 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
       48.49        29.85       102.67        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2744 
       11.34        25.28        25.41        36.16        34.59         0.99 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2767 TCGA-66-2770 
        2.01         0.99        43.99        21.01         2.01        23.01 
TCGA-66-2777 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
        2.01        24.95        40.01         5.03        30.02        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-A59J 
        4.01        49.05         2.73         6.64         8.02        14.73 
TCGA-77-6842 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-8007 TCGA-77-8131 
       29.56        11.18        89.98        20.78         6.51        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ 
       53.92        39.09       104.09        54.41         0.33       126.18 
TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 
      117.57        42.08        30.81        27.62         9.67        12.99 
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        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       16.87        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-90-6837 
        7.76        13.94        12.59        24.36        18.18        24.92 
TCGA-90-7769 TCGA-90-A4ED TCGA-92-8064 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 
       11.77        20.22         5.26         5.03        26.63        16.14 
TCGA-96-7544 TCGA-98-7454 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
       49.87         8.42        27.02        21.21        20.32        18.58 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH 
       19.10        12.89        13.18        64.08         4.54         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HR 
       13.74         4.21         2.89        39.85        37.22        29.75 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A5IB TCGA-XC-AA0X 
        0.43        33.07        11.18         0.20 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           132.36            174.08 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            18.94             20.55 
[1] "0.1 - 132.4 (18.9)" "0.0 - 174.1 (20.6)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         1       60       92        1        39        49
  9P LOSS WILD-TYPE       1       27       59        1        24        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  9P LOSS MUTATED           2         44          8        5
  9P LOSS WILD-TYPE         1         18         13        2
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                60                27
  STAGE IB                92                59
  STAGE II                 1                 1
  STAGE IIA               39                24
  STAGE IIB               49                43
  STAGE III                2                 1
  STAGE IIIA              44                18
  STAGE IIIB               8                13
  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    74 176  42  12
  9P LOSS WILD-TYPE  37 114  27  11
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              74                37
  T2             176               114
  T3              42                27
  T4              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                 N0  N1  N2  N3
  9P LOSS MUTATED   199  75  26   2
  9P LOSS WILD-TYPE 113  56  13   3
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             199               113
  N1              75                56
  N2              26                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   247   5
  9P LOSS WILD-TYPE 157   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    247    5
  9P LOSS WILD-TYPE  157    2
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             247               157
  1               5                 2
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    80 224
  9P LOSS WILD-TYPE  47 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     80  224
  9P LOSS WILD-TYPE   47  142
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              80                47
  MALE               224               142
[1] 2 2
[1] FALSE
D58V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                       6
  9P LOSS WILD-TYPE                                     9
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                         0
  9P LOSS WILD-TYPE                                       1
                   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                                         0
  9P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                           296
  9P LOSS WILD-TYPE                                                         174
D58V9, multiclass
                                                             clus
vv                                                            9P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             296
                                                             clus
vv                                                            9P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               174
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     8 296
  9P LOSS WILD-TYPE   5 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8  296
  9P LOSS WILD-TYPE    5  184
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                8                 5
  YES             296               184
[1] 2 2
[1] FALSE
D58V11, continuous
D58V12, continuous
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED   239   6   3  14
  9P LOSS WILD-TYPE 155   6   1   8
D58V13, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             239               155
  R1               6                 6
  R2               3                 1
  RX              14                 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
  9P LOSS MUTATED       6                        21   210
  9P LOSS WILD-TYPE     3                        10   130
D58V14, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   6                 3
  BLACK OR AFRICAN AMERICAN              21                10
  WHITE                                 210               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"
D58V15, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     4 194
  9P LOSS WILD-TYPE   4 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  194
  9P LOSS WILD-TYPE    4  115
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO             194               115
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   147  87
  9Q LOSS WILD-TYPE 134 109
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              234               243 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               87               109 
$`9Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 
       12.20        79.46        23.54        36.07         1.64         6.18 
TCGA-21-1070 TCGA-21-1075 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 
      119.54        70.16       119.80        43.23        31.63        33.93 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       10.82        32.19         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4607 
       27.02        48.82        20.48        35.08        48.33        19.30 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5482 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 
       14.63         0.79        11.74        22.06         7.63        79.53 
TCGA-33-4582 TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASB TCGA-33-AASD 
      103.53        54.44        19.76        27.02         6.94       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 
       44.19        27.16        61.61        31.50        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       65.23        67.79        16.93        30.94        18.15         4.96 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4130 TCGA-37-4135 
       27.19         4.04        26.43        20.91         8.12         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5024 TCGA-39-5028 
        0.39        47.80        74.07        44.75        70.03         1.71 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-43-2576 TCGA-43-3920 TCGA-43-5670 
       27.39        15.58        35.70        40.21        33.11        27.91 
TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 
       24.89         5.46        19.59         7.76        13.38        11.77 
TCGA-43-8118 TCGA-43-A56V TCGA-46-6026 TCGA-51-4081 TCGA-52-7810 TCGA-56-1622 
        2.93        12.03        13.91        29.95        30.35        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        0.10        18.25         2.04         0.62         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        0.99         1.45         1.32         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 
       26.89         1.35         1.81         1.18         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8390 TCGA-58-8392 
       15.81        20.94        21.04         0.26        29.95        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 
       34.78        85.12         3.58        10.22        96.82        92.71 
TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       80.45         9.01        50.33        42.64         3.19        32.32 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MH 
       35.90        23.57        26.83        11.77        70.62        66.61 
TCGA-63-A5MI TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       58.65        78.28        16.37        36.16        53.88        34.59 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 TCGA-66-2759 
       43.10         2.01        21.07         1.02         0.92        25.05 
TCGA-66-2763 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
        0.99         7.07        19.00         3.02        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        3.98        12.00         1.97        22.98         4.04        22.98 
TCGA-66-2793 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
       10.06         6.94         8.02        13.35        16.18        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 
       73.12        75.09        23.28       106.95        46.78         6.51 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       86.76        37.81        82.92        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G6 
       26.40         6.97         9.63        35.90       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7843 
        5.92        42.41        38.86        11.97        34.95         1.15 
TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       25.15         0.76        13.22        22.45        16.77         5.29 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50M 
        0.10        15.62        17.72        14.96        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-7766 
       16.21        15.85        14.96         0.79        12.39         9.50 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
        2.93        14.07        22.62        10.59         2.70         3.48 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8491 
        2.30        21.04         0.16        11.70         4.01        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-8020 
       14.14        17.69        49.87        18.31        17.46         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B 
       30.81        30.67        21.34        27.16         3.88         2.01 
TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       12.89        13.41         0.07         4.54        51.78        45.37 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CT 
       39.85        37.22        24.00        14.73        22.78        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
        3.65        16.80         3.72        43.89         8.58        11.18 

$`9Q LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
        7.46        75.75         4.80       117.57        11.34        92.15 
TCGA-18-3416 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
       31.99        86.96         2.79       154.32        49.94        27.19 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       46.88        99.16        60.89        34.78        15.58        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 
      122.43         9.34        88.11        41.69        21.99         7.33 
TCGA-22-1000 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       14.93        24.13         0.56        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       32.02         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
       44.25        54.28        71.34        79.20        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
       62.86        56.32        16.64       133.74        98.01       174.08 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      151.27        14.07         1.55         4.70         0.30        36.62 
TCGA-33-AASJ TCGA-34-2596 TCGA-34-2605 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
      118.36         2.63        28.96        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-7107 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       12.00         1.12         3.95         0.43         0.39         6.58 
TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 
        7.46         7.82         3.39        68.58        55.20        60.79 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 
       24.33         1.94        36.39        35.64        17.88        17.06 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-6143 TCGA-43-6770 
       22.49        38.66        27.02        18.38        12.36        21.47 
TCGA-43-6773 TCGA-43-7658 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 
        3.81        66.51        11.61         9.73        14.20         9.99 
TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 
       10.65         0.39         0.39        28.34         5.46         8.75 
TCGA-52-7812 TCGA-56-7582 TCGA-56-7730 TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 
       27.45         0.85         6.51        17.00        14.07        16.77 
TCGA-56-8623 TCGA-56-8625 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK 
       22.75        10.36        19.23        13.32        17.85        18.74 
TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 
        0.13         2.76         0.03        13.25        13.55        71.24 
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-60-2704 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
       37.94        21.93        49.48        66.54        41.42        56.91 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML 
       35.34        48.49        29.85       102.67        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MU TCGA-66-2727 
       14.99        11.34        25.28        89.29        25.41        16.96 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2765 
        0.99         2.01         0.99        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-77-7138 TCGA-77-7139 
       49.05         2.73         6.64        14.73        11.18        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7465 
       20.78         0.49        42.28        70.13         0.16        15.75 
TCGA-77-8009 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8144 TCGA-77-8150 
       53.95        12.59        53.92        39.09        27.39        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GB 
       65.49         0.33       126.18       117.57        42.08        30.81 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
       27.62         9.67        12.99         6.41        36.53        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
       32.91         1.38        29.95        18.94        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8353 
       31.56        14.07        16.87        34.52        10.09         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       32.71         2.01         0.72         7.76        14.63        13.94 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A5B5 
       12.59        25.68        19.33        24.36        18.18         3.65 
TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8064 TCGA-94-8490 
       24.92        11.77        20.22         4.01         5.26         5.03 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53A 
       16.14        57.07        19.36        16.57         8.42        18.15 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       27.02        21.21        20.32        18.58        20.71        19.10 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HJ 
       16.11        13.18        11.84        64.08         1.22        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A7XE 
        4.21         2.89        30.58        29.75        83.57         0.43 
TCGA-O2-A52N TCGA-O2-A52S TCGA-XC-AA0X 
       33.07        12.72         0.20 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           132.36            174.08 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            18.28             19.36 
[1] "0.1 - 132.4 (18.3)" "0.0 - 174.1 (19.4)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         1       48       63        1        32        48
  9Q LOSS WILD-TYPE       1       39       88        1        31        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  9Q LOSS MUTATED           2         31          7        5
  9Q LOSS WILD-TYPE         1         31         14        2
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                48                39
  STAGE IB                63                88
  STAGE II                 1                 1
  STAGE IIA               32                31
  STAGE IIB               48                44
  STAGE III                2                 1
  STAGE IIIA              31                31
  STAGE IIIB               7                14
  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    59 137  38   7
  9Q LOSS WILD-TYPE  52 153  31  16
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              59                52
  T2             137               153
  T3              38                31
  T4               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                 N0  N1  N2  N3
  9Q LOSS MUTATED   152  68  17   2
  9Q LOSS WILD-TYPE 160  63  22   3
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             152               160
  N1              68                63
  N2              17                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"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   191   5
  9Q LOSS WILD-TYPE 213   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    191    5
  9Q LOSS WILD-TYPE  213    2
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             191               213
  1               5                 2
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    63 178
  9Q LOSS WILD-TYPE  64 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     63  178
  9Q LOSS WILD-TYPE   64  188
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              63                64
  MALE               178               188
[1] 2 2
[1] FALSE
D59V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                       4
  9Q LOSS WILD-TYPE                                    11
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                         1
  9Q LOSS WILD-TYPE                                       0
                   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                                                           234
  9Q LOSS WILD-TYPE                                                         236
D59V9, multiclass
                                                             clus
vv                                                            9Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG CLEAR CELL 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)             234
                                                             clus
vv                                                            9Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               236
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     4 237
  9Q LOSS WILD-TYPE   9 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4  237
  9Q LOSS WILD-TYPE    9  243
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                4                 9
  YES             237               243
[1] 2 2
[1] FALSE
D59V11, continuous
D59V12, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED   188   3   2   8
  9Q LOSS WILD-TYPE 206   9   2  14
D59V13, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0             188               206
  R1               3                 9
  R2               2                 2
  RX               8                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   165
  9Q LOSS WILD-TYPE     4                        13   175
D59V14, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   5                 4
  BLACK OR AFRICAN AMERICAN              18                13
  WHITE                                 165               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"
D59V15, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1 156
  9Q LOSS WILD-TYPE   7 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1  156
  9Q LOSS WILD-TYPE    7  153
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO             156               153
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED   122  81
  10P LOSS WILD-TYPE 159 115
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               203                274 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                81                115 
$`10P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3411 TCGA-18-3412 TCGA-18-3421 TCGA-18-4083 TCGA-18-5592 
       12.20       117.57        11.34        86.96         6.18        49.94 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
       27.19        46.88        99.16        70.16        60.89        34.78 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 
       31.73       122.43       119.80        33.93        32.19        21.99 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       14.93        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-33-4533 
        0.79        54.28        11.74        18.84        56.32       133.74 
TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-A5GW TCGA-33-AAS8 
       98.01       103.53       151.27        14.07         0.30        36.62 
TCGA-33-AASD TCGA-34-2596 TCGA-34-2605 TCGA-34-5236 TCGA-34-5927 TCGA-34-8456 
      110.99         2.63        28.96         9.07        30.94        26.43 
TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4135 TCGA-37-5819 TCGA-39-5019 
       20.91         0.43         0.39         6.81         3.39        44.75 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 
       68.58        60.79        24.33         1.94        27.39        35.64 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 
       17.88        40.21        22.49        33.11        12.36        21.47 
TCGA-43-8118 TCGA-43-A56U TCGA-43-A56V TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        2.93        14.20        12.03         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         0.99         1.32 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8307 TCGA-56-8503 TCGA-56-8622 TCGA-56-8626 
        0.85         6.51        26.89         1.35         1.81         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T 
       20.25        15.81        20.94        17.85        18.74         2.76 
TCGA-58-8386 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
        0.03        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 
       35.24        21.11        96.82        37.94        80.45        49.48 
TCGA-60-2710 TCGA-60-2715 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       66.54        35.34        42.64        29.85        35.90        26.83 
TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        66.61        58.65        59.97        45.57        14.99 
TCGA-63-A5MP TCGA-66-2727 TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       25.28        16.96         2.01         1.02         2.01         0.92 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2770 TCGA-66-2777 TCGA-66-2786 
       43.99        21.01        25.05        23.01         2.01        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2800 
       40.01        22.98         4.04         5.03        10.06        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 
        2.73         6.64         8.02        13.35        14.73        29.56 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 
       23.28        11.18        89.98        15.75        53.95        82.92 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
       53.92        39.09        17.72       104.09        11.54        27.39 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 
       65.49         0.33        30.81        27.62         6.41        36.53 
TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       32.91        29.95        18.94        24.13        31.56        14.07 
TCGA-85-8277 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 
       10.09        16.77         3.09        32.71         0.72        14.63 
TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-A4EE 
       19.33        14.96        18.18        19.73         3.65        22.62 
TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-A5I4 TCGA-94-A5I6 
        5.26        21.04         0.16         4.01        16.14        17.69 
TCGA-96-8170 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 
       17.46        19.36         2.76        30.81        21.34        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
        3.88        18.15        20.71        19.10        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HR 
       13.41        11.84         0.07        39.85        30.58        29.75 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       65.49        16.80        12.72        43.89        11.18 

$`10P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
        7.46        75.75        79.46         4.80        23.54        92.15 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 
       31.99        36.07         1.64         2.79       154.32       119.54 
TCGA-21-1078 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
       15.58         9.34        43.23        31.63        88.11        41.69 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-1017 TCGA-22-4594 
       10.82         7.33         4.31        14.10        48.82        48.33 
TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 
        0.56        34.75        13.12        32.02        19.30        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 
       64.93        63.55        71.34        79.20        30.12        62.86 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 
       16.64        22.06         7.63        79.53       174.08        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASI 
        1.55        19.76        27.02         4.70         6.94        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 
      118.36        27.16        61.61        31.50        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       65.23        67.79        56.38        23.24        12.00        16.93 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 
       18.15         4.96         1.12        27.19         4.04         3.95 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-39-5011 
        6.58         8.12         7.46         7.82         0.39        47.80 
TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 
       74.07        55.20        70.03         1.71        36.39        15.58 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 
       35.70        17.06        38.66        27.02        18.38        27.91 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
       24.89         5.46         3.81        19.59         7.76        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 
       13.38        11.77        11.61         9.73         9.99        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 
       13.91         0.39         8.75        27.45         0.10         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 
        0.62         0.99         0.43         1.45         0.10        17.49 
TCGA-56-8304 TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8623 TCGA-56-8624 
        3.48        17.00        14.07        16.77        22.75         1.18 
TCGA-56-8625 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
       10.36        19.23        13.32        21.04         0.13         0.26 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46L TCGA-58-A46N TCGA-60-2696 
       13.25        13.55        29.95        56.65        29.92         3.58 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2711 TCGA-60-2712 
       12.23        10.22        92.71        21.93        41.42         9.01 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
       56.91        50.33        48.49         3.19        32.32        23.57 
TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       11.77        70.62        11.34        89.29        78.28        16.37 
TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 
       25.41        36.16        53.88        34.59        43.10        21.07 
TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
        0.99         0.99         0.99         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-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2790 TCGA-66-2792 
        3.98        12.00        24.95         1.97        22.98        30.02 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7757 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 
       54.08         4.01         6.94        16.18        73.12        75.09 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       20.78         0.49        42.28        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8143 
       46.78         6.51        86.76        37.81        12.59        26.40 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
        6.97         9.63        54.41        35.90       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GH 
      117.57        22.29         5.92        42.41        42.08        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
        9.67        11.97        12.99        34.95        31.30         1.38 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
        1.15        25.15        19.04        16.87        34.52         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 
       13.22        22.45         5.29         2.01         7.76        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA 
       12.59         0.10        15.62        25.68        17.72        24.36 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       12.56        16.21        15.85        14.96         0.79        12.39 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
       24.92         9.50         2.93        11.77        14.07        20.22 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7943 
       10.59         2.70         3.48         4.01         2.30        11.70 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
        5.03        26.63        14.14        49.87        57.07        18.31 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       16.57         8.42        30.67         2.01        27.02        21.21 
TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       20.32        18.58        12.89        64.08         4.54        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
        1.22        45.37        13.74         4.21         2.89        37.22 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A7XE 
       24.00        14.73        22.78        83.57         3.65         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52W TCGA-XC-AA0X 
       33.07         3.72         8.58         0.20 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.03               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            151.27             174.08 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             21.34              16.90 
[1] "0.0 - 151.3 (21.3)" "0.1 - 174.1 (16.9)"
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         0       36       74        1        24        38
  10P LOSS WILD-TYPE       2       51       77        1        39        54
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  10P LOSS MUTATED           2         27          7        1
  10P LOSS WILD-TYPE         1         35         14        6
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 36                 51
  STAGE IB                 74                 77
  STAGE II                  1                  1
  STAGE IIA                24                 39
  STAGE IIB                38                 54
  STAGE III                 2                  1
  STAGE IIIA               27                 35
  STAGE IIIB                7                 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
  10P LOSS MUTATED    46 127  29   8
  10P LOSS WILD-TYPE  65 163  40  15
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               46                 65
  T2              127                163
  T3               29                 40
  T4                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                  N0  N1  N2  N3
  10P LOSS MUTATED   137  51  18   2
  10P LOSS WILD-TYPE 175  80  21   3
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0              137                175
  N1               51                 80
  N2               18                 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   177   1
  10P LOSS WILD-TYPE 227   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    177    1
  10P LOSS WILD-TYPE  227    6
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0              177                227
  1                1                  6
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    49 161
  10P LOSS WILD-TYPE  78 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     49  161
  10P LOSS WILD-TYPE   78  205
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               49                 78
  MALE                161                205
[1] 2 2
[1] FALSE
D60V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                       7
  10P LOSS WILD-TYPE                                     8
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                         0
  10P LOSS WILD-TYPE                                       1
                    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                                                           201
  10P LOSS WILD-TYPE                                                         269
D60V9, multiclass
                                                             clus
vv                                                            10P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              201
                                                             clus
vv                                                            10P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                269
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4 206
  10P LOSS WILD-TYPE   9 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  206
  10P LOSS WILD-TYPE    9  274
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 4                  9
  YES              206                274
[1] 2 2
[1] FALSE
D60V11, continuous
D60V12, continuous
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED   172   5   0  11
  10P LOSS WILD-TYPE 222   7   4  11
D60V13, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0              172                222
  R1                5                  7
  R2                0                  4
  RX               11                 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   146
  10P LOSS WILD-TYPE     7                        16   194
D60V14, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               15                 16
  WHITE                                  146                194
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4 134
  10P LOSS WILD-TYPE   4 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  134
  10P LOSS WILD-TYPE    4  175
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              134                175
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   133  84
  10Q LOSS WILD-TYPE 148 112
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               217                260 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                84                112 
$`10Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-4083 TCGA-18-4721 
       12.20         7.46       117.57        11.34         6.18       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-21-1082 TCGA-21-5783 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
      119.80        88.11        32.19        21.99         7.33        14.93 
TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4609 
       64.21         1.74        35.08        24.13        38.17         9.57 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 
       14.63        44.25         0.79        54.28        11.74        18.84 
TCGA-22-5491 TCGA-33-4533 TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 
       56.32       133.74        98.01       151.27        14.07        27.02 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 
        0.30        36.62         6.94       110.99       118.36         2.63 
TCGA-34-2605 TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-8456 TCGA-34-A5IX 
       28.96         9.07        30.94         4.96        26.43        20.91 
TCGA-37-3792 TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        0.39         6.81         3.39        74.07        44.75        68.58 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5039 
       60.79        24.33         1.94        27.39        35.64        17.88 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-6770 TCGA-43-7658 
       40.21        22.49        27.02        33.11        21.47        66.51 
TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
       11.61        14.20        12.03        10.65         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 
       29.95        28.34         5.46        30.35        28.96        18.25 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 
        0.99         0.99         1.32         0.85         6.51         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8628 TCGA-56-8629 
       26.89        14.07         1.35         1.81        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 
       20.94        13.32        17.85        18.74         2.76         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-A46M TCGA-60-2695 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       35.24        21.11        37.94        80.45        49.48        66.54 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
        9.01        35.34        42.64        29.85        35.90        26.83 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
      102.67        70.62        66.61        58.65        59.97        45.57 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 
       16.96         2.01         1.02         2.01        43.99        21.01 
TCGA-66-2759 TCGA-66-2770 TCGA-66-2773 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 
       25.05        23.01         3.02        12.00         1.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 
       22.98         4.04         5.03        30.02        10.06        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 
        2.73         6.64         6.94        13.35        14.73        29.56 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8133 
       11.18        89.98        46.78        15.75        53.95        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-77-8148 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GB TCGA-77-A5GF 
        9.63        65.49         0.33       117.57        30.81        27.62 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7844 
       11.97         6.41        36.53        31.30        32.91        29.95 
TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 TCGA-85-8351 TCGA-85-8353 
       18.94        24.13        31.56        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         0.72        14.63        19.33        14.96        18.18 
TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-A4EE TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 
       19.73         3.65        22.62         5.26        21.04         0.16 
TCGA-94-8035 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK 
        4.01        16.14        17.69        57.07        17.46        19.36 
TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53J 
       30.81        21.34        27.16         3.88        18.15        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       19.10        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HD TCGA-NC-A5HI TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HR 
        0.07        45.37        39.85        37.22        30.58        29.75 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5D1 TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       22.78        83.57        16.80        43.89         8.58        11.18 
TCGA-XC-AA0X 
        0.20 

$`10Q LOSS WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
       75.75        79.46         4.80        23.54        92.15        31.99 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 
       36.07         1.64        86.96         2.79        27.19       119.54 
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-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 
       41.69        33.93        10.82         4.31        14.10        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 
       48.82        20.48        48.33         0.56        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       32.02        19.30        11.77        31.73        64.93        63.55 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 
       71.34        79.20        30.12        62.86        16.64        22.06 
TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 
        7.63        79.53       174.08       103.53        54.44         1.55 
TCGA-33-6737 TCGA-33-A4WN TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 
       19.76         4.70        44.19        27.16        61.61        31.50 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
       32.88        31.27        65.23        67.79        56.38        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       12.00        16.93        18.15         1.12        27.19         4.04 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        3.95         0.43         6.58         8.12         7.46         7.82 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5034 
        0.39        47.80        55.20        70.03         1.71        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 
       15.58        35.70        17.06        38.66        18.38        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
       12.36        24.89         5.46         3.81        19.59         7.76 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-46-3768 TCGA-46-6026 
       13.38        11.77         2.93         9.73         9.99        13.91 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 
        8.75        27.45         0.10         2.04         0.62         0.43 
TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 TCGA-56-8308 TCGA-56-8504 TCGA-56-8623 
        1.45         0.10        17.49        17.00        16.77        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A5DR 
        1.18        10.36         9.93        19.23        21.04         0.13 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8390 TCGA-58-A46L TCGA-58-A46N TCGA-60-2696 
        0.26        13.25        29.95        56.65        29.92         3.58 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2711 
       12.23        10.22        96.82        92.71        21.93        41.42 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
       56.91        50.33        48.49         3.19        32.32        23.57 
TCGA-60-2726 TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       11.77        14.99        11.34        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 
       16.37        25.41        36.16        53.88        34.59        43.10 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 
       21.07         0.99         0.92         0.99         0.99         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 
        1.02         2.01         2.01         7.07        19.00         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2790 
       19.00        12.03         3.98        24.95        25.97        22.98 
TCGA-66-2794 TCGA-66-2795 TCGA-68-8250 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 
       54.08         4.01         8.02        16.18        73.12        75.09 
TCGA-77-6845 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       23.28        20.78         0.49        42.28        70.13       106.95 
TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        0.16         6.51        86.76        37.81        82.92        12.59 
TCGA-77-8145 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
        6.97        54.41        35.90       126.18       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 
        5.92        42.41        42.08        38.86         9.67        12.99 
TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 
       34.95         1.38         1.15        25.15        19.04        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 
       16.87        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        13.94        12.59         0.10        15.62 
TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       25.68        17.72        24.36        12.56        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
       14.96         0.79        12.39        24.92         9.50         2.93 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       11.77        14.07        20.22        10.59         2.70         3.48 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7943 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        4.01         2.30        11.70         5.03        26.63        14.14 
TCGA-96-7544 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 
       49.87        18.31        16.57         8.42         2.76        30.67 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-NC-A5HE 
        2.01        27.02        21.21        20.32        18.58        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54        51.78         1.22        13.74         4.21         2.89 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N 
       24.00        14.73        65.49         3.65         0.43        33.07 
TCGA-O2-A52Q TCGA-O2-A52S 
        3.72        12.72 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.03               0.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            154.32             174.08 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            21.040             17.275 
[1] "0.0 - 154.3 (21.0)" "0.1 - 174.1 (17.3)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         1       37       80        1        29        37
  10Q LOSS WILD-TYPE       1       50       71        1        34        55
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  10Q LOSS MUTATED           1         29          7        1
  10Q LOSS WILD-TYPE         2         33         14        6
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 37                 50
  STAGE IB                 80                 71
  STAGE II                  1                  1
  STAGE IIA                29                 34
  STAGE IIB                37                 55
  STAGE III                 1                  2
  STAGE IIIA               29                 33
  STAGE IIIB                7                 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
  10Q LOSS MUTATED    49 139  30   6
  10Q LOSS WILD-TYPE  62 151  39  17
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               49                 62
  T2              139                151
  T3               30                 39
  T4                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                  N0  N1  N2  N3
  10Q LOSS MUTATED   147  56  17   2
  10Q LOSS WILD-TYPE 165  75  22   3
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0              147                165
  N1               56                 75
  N2               17                 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   184   1
  10Q LOSS WILD-TYPE 220   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    184    1
  10Q LOSS WILD-TYPE  220    6
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              184                220
  1                1                  6
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    50 174
  10Q LOSS WILD-TYPE  77 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     50  174
  10Q LOSS WILD-TYPE   77  192
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               50                 77
  MALE                174                192
[1] 2 2
[1] FALSE
D61V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                       8
  10Q LOSS WILD-TYPE                                     7
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                         0
  10Q LOSS WILD-TYPE                                       1
                    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                                                           214
  10Q LOSS WILD-TYPE                                                         256
D61V9, multiclass
                                                             clus
vv                                                            10Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              214
                                                             clus
vv                                                            10Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                256
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4 220
  10Q LOSS WILD-TYPE   9 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  220
  10Q LOSS WILD-TYPE    9  260
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 4                  9
  YES              220                260
[1] 2 2
[1] FALSE
D61V11, continuous
D61V12, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED   185   4   0   9
  10Q LOSS WILD-TYPE 209   8   4  13
D61V13, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0              185                209
  R1                4                  8
  R2                0                  4
  RX                9                 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   152
  10Q LOSS WILD-TYPE     6                        13   188
D61V14, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN               18                 13
  WHITE                                  152                188
[1] 3 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     4 139
  10Q LOSS WILD-TYPE   4 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  139
  10Q LOSS WILD-TYPE    4  170
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              139                170
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED   100  69
  11P LOSS WILD-TYPE 181 127
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               169                308 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                69                127 
$`11P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
       12.20        79.46        11.34        23.54        36.07        86.96 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       46.88        60.89       122.43       119.80        43.23        31.63 
TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 
       33.93        10.82         4.31        48.82        35.08         0.56 
TCGA-22-4601 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       34.75        31.73        63.55        44.25         0.79        54.28 
TCGA-22-5481 TCGA-22-5483 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       79.20        18.84        22.06       133.74        98.01        79.53 
TCGA-33-4587 TCGA-33-6737 TCGA-33-AASB TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 
       54.44        19.76         6.94        44.19         2.63        61.61 
TCGA-34-2605 TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5928 TCGA-34-5929 
       28.96        65.23        67.79         9.07        18.15         4.96 
TCGA-37-3789 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 
        0.43         8.12         7.46         6.81         0.39        47.80 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 
       44.75        68.58        55.20        27.39        15.58        35.70 
TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 TCGA-43-A56V 
       38.66        33.11        12.36         7.76        66.51        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
        9.99        10.65         0.39         0.99         0.43         1.45 
TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8628 
        1.32        17.49         1.35        16.77         1.18        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T 
       15.81        19.23        21.04        18.74         0.13         2.76 
TCGA-58-8387 TCGA-58-8390 TCGA-60-2695 TCGA-60-2698 TCGA-60-2708 TCGA-60-2712 
       13.25        29.95        21.11        10.22        80.45         9.01 
TCGA-60-2714 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 
       50.33         3.19        32.32        35.90        23.57        11.77 
TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-66-2742 TCGA-66-2758 TCGA-66-2759 
       66.61        59.97        45.57        21.07        21.01        25.05 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 
        2.01         2.01        19.00         3.02        12.03         3.98 
TCGA-66-2782 TCGA-66-2793 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J 
       12.00        10.06         6.94         8.02        13.35        14.73 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 
       75.09        89.98         0.49         0.16        15.75        86.76 
TCGA-77-8009 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       53.95        53.92        17.72        11.54        26.40        27.39 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA 
        9.63        54.41        65.49        22.29        42.41        42.08 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 
       27.62        12.99        36.53        32.91         1.15        25.15 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 TCGA-85-A4CN 
       10.09        13.22         5.29         3.09         0.72        19.33 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7964 
       14.96        18.18        19.73        15.85         3.65        14.07 
TCGA-90-A59Q TCGA-94-8035 TCGA-94-8490 TCGA-94-A5I6 TCGA-96-7545 TCGA-98-8020 
       10.59         4.01         5.03        17.69        57.07         2.76 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53J TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
       21.34        27.16        20.71        13.41        11.84         0.07 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HR 
       64.08        51.78        13.74        37.22        14.73        29.75 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V 
       83.57        65.49        16.80        33.07         3.72        43.89 
TCGA-O2-A52W 
        8.58 

$`11P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 
        7.46        75.75         4.80       117.57        92.15        31.99 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1.64         6.18         2.79       154.32        49.94        27.19 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
      119.54        99.16        70.16        34.78        15.58        31.73 
TCGA-21-1081 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
        9.34        88.11        41.69        32.19        21.99         7.33 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
       14.93        64.21         1.74        14.10        27.02        20.48 
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-22-4613 TCGA-22-5472 TCGA-22-5474 TCGA-22-5480 TCGA-22-5482 
        9.57        11.77        64.93        14.63        71.34        11.74 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4566 
       30.12        62.86        56.32        16.64         7.63       174.08 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07         1.55        27.02         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2604 
        0.30        36.62       110.99       118.36        27.16        31.50 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       32.88        31.27        56.38        23.24        12.00        16.93 
TCGA-34-5927 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       30.94         1.12        27.19         4.04        26.43        20.91 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4133 TCGA-37-5819 TCGA-39-5016 
        3.95         0.39         6.58         7.82         3.39        74.07 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
       70.03        60.79         1.71        24.33         1.94        36.39 
TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 
       35.64        17.88        17.06        40.21        22.49        27.02 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       18.38        27.91        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
       19.59        13.38        11.77         2.93        11.61         9.73 
TCGA-43-A56U TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       14.20        13.91         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         0.10        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        2.04         0.62         0.99         0.85         6.51         0.10 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 
        3.48        26.89        17.00        14.07         1.81        22.75 
TCGA-56-8625 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS 
       10.36         9.93        20.94        13.32        17.85         0.26 
TCGA-58-8386 TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
        0.03        13.55        71.24        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 
       34.36        56.65        35.24        29.92         3.58        12.23 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
       96.82        37.94        92.71        21.93        49.48        66.54 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2722 
       41.42        56.91        35.34        48.49        42.64        29.85 
TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN 
       26.83       102.67        70.62        58.65        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV 
       25.28        89.29        78.28        16.37        25.41        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 
       53.88        34.59        16.96        43.10         2.01         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 
        1.02         2.01         0.92         0.99        43.99         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2778 
        2.01         1.02         7.07        23.01         2.01        19.00 
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-66-2792 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-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 
        2.73         6.64        16.18        29.56        73.12        23.28 
TCGA-77-7138 TCGA-77-7140 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
       11.18        20.78        42.28        70.13       106.95        46.78 
TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 
        6.51        37.81        82.92        12.59        39.09       104.09 
TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        6.97        35.90         0.33       126.18       132.36       117.57 
TCGA-77-A5G7 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 
        5.92        30.81        38.86         9.67        11.97         6.41 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
       34.95        31.30         1.38        29.95        18.94        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
       24.13        31.56        14.07        16.87        34.52         0.76 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
       22.45        16.77        32.71         2.01         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB 
       13.94        12.59         0.10        15.62        25.68        17.72 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       24.36        12.56        16.21        14.96         0.79        12.39 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
       24.92         9.50         2.93        11.77        20.22        22.62 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
        2.70         3.48         4.01         5.26         2.30        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 
        0.16        11.70        26.63        14.14        16.14        49.87 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       18.31        17.46        19.36        16.57         8.42        30.81 
TCGA-98-8022 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       30.67         3.88        18.15         2.01        27.02        21.21 
TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       20.32        18.58        19.10        12.89        16.11        13.18 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
        4.54         1.22        45.37         4.21         2.89        39.85 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52S 
       30.58        24.00        22.78         3.65         0.43        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 
            133.74             174.08 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             19.23              19.07 
[1] "0.1 - 133.7 (19.2)" "0.0 - 174.1 (19.1)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         2       25       54        1        22        30
  11P LOSS WILD-TYPE       0       62       97        1        41        62
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  11P LOSS MUTATED           1         24          4        4
  11P LOSS WILD-TYPE         2         38         17        3
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 25                 62
  STAGE IB                 54                 97
  STAGE II                  1                  1
  STAGE IIA                22                 41
  STAGE IIB                30                 62
  STAGE III                 1                  2
  STAGE IIIA               24                 38
  STAGE IIIB                4                 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
  11P LOSS MUTATED    33 105  27   5
  11P LOSS WILD-TYPE  78 185  42  18
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               33                 78
  T2              105                185
  T3               27                 42
  T4                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                  N0  N1  N2  N3
  11P LOSS MUTATED   107  51  10   1
  11P LOSS WILD-TYPE 205  80  29   4
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0              107                205
  N1               51                 80
  N2               10                 29
  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   138   4
  11P LOSS WILD-TYPE 266   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    138    4
  11P LOSS WILD-TYPE  266    3
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0              138                266
  1                4                  3
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    40 130
  11P LOSS WILD-TYPE  87 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     40  130
  11P LOSS WILD-TYPE   87  236
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               40                 87
  MALE                130                236
[1] 2 2
[1] FALSE
D62V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                       6
  11P LOSS WILD-TYPE                                     9
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                         0
  11P LOSS WILD-TYPE                                       1
                    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                                                           162
  11P LOSS WILD-TYPE                                                         308
D62V9, multiclass
                                                             clus
vv                                                            11P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              162
                                                             clus
vv                                                            11P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                308
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5 165
  11P LOSS WILD-TYPE   8 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5  165
  11P LOSS WILD-TYPE    8  315
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 5                  8
  YES              165                315
[1] 2 2
[1] FALSE
D62V11, continuous
D62V12, continuous
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED   138   3   1   5
  11P LOSS WILD-TYPE 256   9   3  17
D62V13, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0              138                256
  R1                3                  9
  R2                1                  3
  RX                5                 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
  11P LOSS MUTATED       1                        14   120
  11P LOSS WILD-TYPE     8                        17   220
D62V14, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN               14                 17
  WHITE                                  120                220
[1] 3 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     2 110
  11P LOSS WILD-TYPE   6 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2  110
  11P LOSS WILD-TYPE    6  199
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO              110                199
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    83  57
  11Q LOSS WILD-TYPE 198 139
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               140                337 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                57                139 
$`11Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
       12.20        79.46        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-22-4593 TCGA-22-4601 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
        1.74        35.08        34.75        63.55        44.25         0.79 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-33-AASB TCGA-33-AASL TCGA-34-2596 
      133.74         1.55        19.76         6.94        27.16         2.63 
TCGA-34-2600 TCGA-34-2605 TCGA-34-5232 TCGA-34-5236 TCGA-34-5928 TCGA-37-3789 
       61.61        28.96        67.79         9.07        18.15         0.43 
TCGA-37-4130 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 
        8.12        74.07        44.75        68.58        55.20        60.79 
TCGA-39-5031 TCGA-39-5037 TCGA-43-2581 TCGA-43-3920 TCGA-43-7657 TCGA-43-7658 
       27.39        35.70        38.66        33.11         7.76        66.51 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       11.77        11.61        12.03         9.99        10.65        13.91 
TCGA-51-4079 TCGA-52-7809 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 
        0.39         5.46         0.99         0.43         0.99         1.32 
TCGA-56-7822 TCGA-56-8504 TCGA-56-8624 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
       17.49        16.77         1.18        15.81        19.23        13.32 
TCGA-56-A4ZK TCGA-58-8387 TCGA-58-8390 TCGA-60-2695 TCGA-60-2698 TCGA-60-2708 
       18.74        13.25        29.95        21.11        10.22        80.45 
TCGA-60-2712 TCGA-60-2714 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
        9.01        50.33        29.85        35.90        26.83        11.77 
TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-66-2758 TCGA-66-2767 
       66.61        59.97        45.57        78.28        21.01         2.01 
TCGA-66-2768 TCGA-66-2790 TCGA-66-2793 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J 
        2.01        22.98        10.06         8.02        13.35        14.73 
TCGA-77-7139 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 
       89.98         0.16        15.75        86.76        53.95        82.92 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 
       53.92        39.09        17.72        26.40        27.39         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GF TCGA-85-6561 
       54.41        65.49       117.57        22.29        27.62        12.99 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-8048 TCGA-85-8072 TCGA-85-8277 
        6.41        36.53        32.91        25.15        16.87        10.09 
TCGA-85-8352 TCGA-85-8479 TCGA-85-8664 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
        5.29         0.72         0.10        14.96        18.18        19.73 
TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7341 
       14.96         3.65         9.50        14.07        10.59         3.48 
TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JL TCGA-98-8020 TCGA-98-8023 TCGA-98-A538 
       17.69        57.07        16.57         2.76        21.34        27.16 
TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HJ 
       20.71        11.84         0.07        64.08        51.78        13.74 
TCGA-NC-A5HO TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52V 
       30.58        83.57        65.49        16.80        33.07        43.89 
TCGA-O2-A52W TCGA-O2-A5IB 
        8.58        11.18 

$`11Q LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 
        7.46        75.75         4.80       117.57        92.15        31.99 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1.64         6.18         2.79       154.32        49.94        27.19 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
      119.54        46.88        99.16        70.16        34.78        15.58 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
       31.73         9.34       119.80        31.63        41.69        33.93 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1012 
       32.19        21.99         7.33        14.93        64.21        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       27.02        48.82        20.48        48.33        24.13         0.56 
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-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       31.73        64.93        14.63        54.28        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-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       22.06         7.63        98.01        79.53       174.08       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
      151.27        14.07        54.44        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2604 TCGA-34-2608 
       36.62       110.99        44.19       118.36        31.50        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       31.27        65.23        56.38        23.24        12.00        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       30.94         4.96         1.12        27.19         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
       20.91         3.95         0.39         6.58         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5024 TCGA-39-5028 
        6.81         0.39         3.39        47.80        70.03         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 
       24.33         1.94        36.39        15.58        35.64        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 
       17.06        40.21        22.49        27.02        18.38        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       12.36        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-51-4080 TCGA-51-4081 
       13.38         2.93         9.73        14.20         0.39        29.95 
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         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
       18.25         2.04         0.62         1.45         0.85         6.51 
TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 
        0.10         3.48        26.89        17.00        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-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       17.85        21.04         0.13         0.26         2.76         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-60-2696 TCGA-60-2697 TCGA-60-2703 
       56.65        35.24        29.92         3.58        12.23        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       37.94        92.71        21.93        49.48        66.54        41.42 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       56.91        35.34        48.49        42.64         3.19        32.32 
TCGA-60-2724 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN 
       23.57       102.67        70.62        58.65        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       25.28        89.29        16.37        25.41        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-66-2759 
        1.02         2.01         0.92         0.99        43.99        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
        0.99         2.01         1.02         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-66-2791 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-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
        6.64         6.94        16.18        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       23.28        11.18        20.78         0.49        42.28        70.13 
TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-8139 
      106.95        46.78         6.51        37.81        12.59       104.09 
TCGA-77-8140 TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       11.54         6.97        35.90         0.33       126.18       132.36 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 
        5.92        42.41        42.08        30.81        38.86         9.67 
TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       11.97        34.95        31.30         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
       18.94        19.04        24.13        31.56        14.07        34.52 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
        0.76        13.22        22.45        16.77         3.09        32.71 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 
        2.01         7.76        14.63        13.94        12.59        15.62 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z 
       25.68        19.33        17.72        24.36        12.56        16.21 
TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
       15.85         0.79        12.39        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-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
       21.04         0.16        11.70         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       14.14        16.14        49.87        18.31        17.46        19.36 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
        8.42        30.81        30.67         3.88        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 
       27.02        21.21        20.32        18.58        19.10        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        45.37 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.21         2.89        39.85        37.22        24.00        14.73 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52S 
       29.75        22.78         3.65         0.43         3.72        12.72 
TCGA-XC-AA0X 
        0.20 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.07               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            133.74             174.08 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            18.985             19.100 
[1] "0.1 - 133.7 (19.0)" "0.0 - 174.1 (19.1)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         2       20       43        1        18        28
  11Q LOSS WILD-TYPE       0       67      108        1        45        64
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  11Q LOSS MUTATED           1         19          3        2
  11Q LOSS WILD-TYPE         2         43         18        5
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 20                 67
  STAGE IB                 43                108
  STAGE II                  1                  1
  STAGE IIA                18                 45
  STAGE IIB                28                 64
  STAGE III                 1                  2
  STAGE IIIA               19                 43
  STAGE IIIB                3                 18
  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    25  91  19   5
  11Q LOSS WILD-TYPE  86 199  50  18
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               25                 86
  T2               91                199
  T3               19                 50
  T4                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                  N0  N1  N2  N3
  11Q LOSS MUTATED    83  48   7   1
  11Q LOSS WILD-TYPE 229  83  32   4
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               83                229
  N1               48                 83
  N2                7                 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"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   113   2
  11Q LOSS WILD-TYPE 291   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    113    2
  11Q LOSS WILD-TYPE  291    5
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0              113                291
  1                2                  5
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    29 111
  11Q LOSS WILD-TYPE  98 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     29  111
  11Q LOSS WILD-TYPE   98  255
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               29                 98
  MALE                111                255
[1] 2 2
[1] FALSE
D63V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                       6
  11Q LOSS WILD-TYPE                                     9
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                         0
  11Q LOSS WILD-TYPE                                       1
                    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                                                           133
  11Q LOSS WILD-TYPE                                                         337
D63V9, multiclass
                                                             clus
vv                                                            11Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG CLEAR CELL 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)              133
                                                             clus
vv                                                            11Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                337
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     4 136
  11Q LOSS WILD-TYPE   9 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4  136
  11Q LOSS WILD-TYPE    9  344
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 4                  9
  YES              136                344
[1] 2 2
[1] FALSE
D63V11, continuous
D63V12, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED   112   2   1   2
  11Q LOSS WILD-TYPE 282  10   3  20
D63V13, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0              112                282
  R1                2                 10
  R2                1                  3
  RX                2                 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    98
  11Q LOSS WILD-TYPE     7                        19   242
D63V14, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               12                 19
  WHITE                                   98                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"
D63V15, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2  94
  11Q LOSS WILD-TYPE   6 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   94
  11Q LOSS WILD-TYPE    6  215
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               94                215
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    22  16
  12P LOSS WILD-TYPE 259 180
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                38                439 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                16                180 
$`12P LOSS MUTATED`
TCGA-18-3407 TCGA-22-1016 TCGA-22-5478 TCGA-33-4533 TCGA-33-4587 TCGA-33-AASB 
        7.46        27.02         0.79       133.74        54.44         6.94 
TCGA-34-2604 TCGA-34-A5IX TCGA-37-4129 TCGA-37-4130 TCGA-37-4141 TCGA-39-5011 
       31.50        20.91         6.58         8.12         0.39        47.80 
TCGA-43-2581 TCGA-43-5668 TCGA-43-6143 TCGA-43-8118 TCGA-56-5898 TCGA-56-7579 
       38.66        18.38        12.36         2.93        18.25         1.45 
TCGA-56-8624 TCGA-56-A49D TCGA-56-A4ZK TCGA-60-2722 TCGA-66-2773 TCGA-77-7138 
        1.18        20.94        18.74        29.85         3.02        11.18 
TCGA-77-8008 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5GA TCGA-85-6798 TCGA-85-8353 
       86.76        54.41        65.49        42.08         6.41         3.09 
TCGA-85-8479 TCGA-85-A4JB TCGA-85-A50M TCGA-85-A5B5 TCGA-90-A4ED TCGA-NC-A5HL 
        0.72        17.72        12.56         3.65        20.22         2.89 
TCGA-NK-A5CR TCGA-O2-A52V 
       83.57        43.89 

$`12P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
       12.20        75.75        79.46         4.80       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       23.54        92.15        31.99        36.07         1.64        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
        6.18         2.79       154.32        49.94        27.19       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-21-A5DI TCGA-22-0940 
       88.11        41.69        33.93        10.82        32.19        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
        7.33        14.93         4.31        64.21         1.74        14.10 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       48.82        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-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       11.77        31.73        64.93        63.55        14.63        44.25 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       54.28        71.34        79.20        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
       62.86        56.32        16.64        22.06         7.63        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 
       79.53       174.08       103.53       151.27        14.07         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD 
       19.76        27.02         4.70         0.30        36.62       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
       44.19       118.36        27.16         2.63        61.61        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       32.88        31.27        65.23        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       23.24        12.00        16.93        30.94        18.15         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 
        1.12        27.19         4.04        26.43         3.95         0.43 
TCGA-37-3792 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 
        0.39         7.46         7.82         6.81         3.39        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
       44.75        68.58        55.20        70.03        60.79         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        27.39        36.39        15.58        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 
       35.70        17.88        17.06        40.21        22.49        27.02 
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-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 
       19.59         7.76        66.51        13.38        11.77        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
        9.73        14.20        12.03         9.99        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-56-6546 
        8.75        27.45        28.96         0.10         2.04         0.62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
        0.99         0.43         0.99         1.32         0.85         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.10        17.49         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 
        1.35        16.77         1.81        22.75        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
       20.25        15.81        19.23        13.32        17.85        21.04 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         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-60-2696 TCGA-60-2697 
       56.65        35.24        29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
       49.48        66.54        41.42         9.01        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 
       35.34        48.49        42.64         3.19        32.32        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH 
       23.57        26.83        11.77       102.67        70.62        66.61 
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-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       89.29        78.28        16.37        25.41        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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
        8.02        13.35        16.18        14.73        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       75.09        23.28        89.98        20.78         0.49        42.28 
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        15.75         6.51 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       53.95        37.81        82.92        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 
        9.63        35.90         0.33       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
       22.29         5.92        42.41        30.81        27.62        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
        9.67        11.97        12.99        36.53        34.95        31.30 
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-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       19.04        24.13        31.56        14.07        16.87        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-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
       32.71         2.01         7.76        14.63        13.94        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA 
        0.10        15.62        25.68        19.33        14.96        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       18.18        19.73        16.21        15.85        14.96         0.79 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
       12.39        24.92         9.50         2.93        11.77        14.07 
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-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.30        21.04         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       26.63        14.14        16.14        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       18.31        17.46        19.36        16.57         8.42         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
       30.81        30.67        21.34        27.16         3.88        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
        2.01        27.02        21.21        20.32        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       19.10        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
        0.07        64.08         4.54        51.78         1.22        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21        39.85        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       14.73        29.75        22.78        65.49         3.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52W TCGA-O2-A5IB 
        0.43        33.07         3.72        12.72         8.58        11.18 
TCGA-XC-AA0X 
        0.20 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.39               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            133.74             174.08 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            17.985             19.330 
[1] "0.4 - 133.7 (18.0)" "0.0 - 174.1 (19.3)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         0        6       18        1         3         4
  12P LOSS WILD-TYPE       2       81      133        1        60        88
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  12P LOSS MUTATED           0          6          0        0
  12P LOSS WILD-TYPE         3         56         21        7
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  6                 81
  STAGE IB                 18                133
  STAGE II                  1                  1
  STAGE IIA                 3                 60
  STAGE IIB                 4                 88
  STAGE III                 0                  3
  STAGE IIIA                6                 56
  STAGE IIIB                0                 21
  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   0
  12P LOSS WILD-TYPE 102 270  60  23
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                9                102
  T2               20                270
  T3                9                 60
  T4                0                 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   1   0
  12P LOSS WILD-TYPE 282 124  38   5
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               30                282
  N1                7                124
  N2                1                 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    31   0
  12P LOSS WILD-TYPE 373   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     31    0
  12P LOSS WILD-TYPE  373    7
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               31                373
  1                0                  7
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    11  27
  12P LOSS WILD-TYPE 116 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     11   27
  12P LOSS WILD-TYPE  116  339
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               11                116
  MALE                 27                339
[1] 2 2
[1] FALSE
D64V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                       1
  12P LOSS WILD-TYPE                                    14
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                         0
  12P LOSS WILD-TYPE                                       1
                    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                                                            35
  12P LOSS WILD-TYPE                                                         435
D64V9, multiclass
                                                             clus
vv                                                            12P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               35
                                                             clus
vv                                                            12P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                435
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  38
  12P LOSS WILD-TYPE  13 442
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   38
  12P LOSS WILD-TYPE   13  442
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                 13
  YES               38                442
[1] 2 2
[1] FALSE
D64V11, continuous
D64V12, continuous
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    30   1   0   1
  12P LOSS WILD-TYPE 364  11   4  21
D64V13, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               30                364
  R1                1                 11
  R2                0                  4
  RX                1                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       2                         3    25
  12P LOSS WILD-TYPE     7                        28   315
D64V14, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                   25                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"
D64V15, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  29
  12P LOSS WILD-TYPE   8 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   29
  12P LOSS WILD-TYPE    8  280
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               29                280
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    29  18
  12Q LOSS WILD-TYPE 252 178
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                47                430 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                18                178 
$`12Q LOSS MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-22-4595 TCGA-22-5478 TCGA-33-4533 
        7.46        75.75        79.46        24.13         0.79       133.74 
TCGA-33-4587 TCGA-34-2604 TCGA-34-A5IX TCGA-37-4129 TCGA-37-4141 TCGA-43-2581 
       54.44        31.50        20.91         6.58         0.39        38.66 
TCGA-43-5668 TCGA-43-6143 TCGA-43-8118 TCGA-43-A56V TCGA-51-4081 TCGA-52-7810 
       18.38        12.36         2.93        12.03        29.95        30.35 
TCGA-56-5898 TCGA-56-8624 TCGA-56-A49D TCGA-60-2703 TCGA-60-2722 TCGA-60-2723 
       18.25         1.18        20.94        96.82        29.85        35.90 
TCGA-66-2773 TCGA-68-8250 TCGA-77-7138 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 
        3.02         8.02        11.18         6.51        86.76        12.59 
TCGA-77-8153 TCGA-77-A5GA TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-8479 
       65.49        42.08        11.97         6.41        36.53         0.72 
TCGA-85-A4JB TCGA-85-A50M TCGA-90-A4ED TCGA-94-A4VJ TCGA-94-A5I6 TCGA-98-A538 
       17.72        12.56        20.22        14.14        17.69        27.16 
TCGA-98-A53J TCGA-MF-A522 TCGA-NK-A5CR TCGA-O2-A52V TCGA-O2-A52W 
       20.71        11.84        83.57        43.89         8.58 

$`12Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       12.20         4.80       117.57        11.34        23.54        92.15 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       31.99        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
      154.32        49.94        27.19       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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       33.93        10.82        32.19        21.99         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
        4.31        64.21         1.74        14.10        27.02        48.82 
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-22-5471 
       13.12        32.02        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
       64.93        63.55        14.63        44.25        54.28        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-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       16.64        22.06         7.63        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      103.53       151.27        14.07         1.55        19.76        27.02 
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-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 
      118.36        27.16         2.63        61.61        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.27        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       12.00        16.93        30.94        18.15         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       27.19         4.04        26.43         3.95         0.43         0.39 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 
        8.12         7.46         7.82         6.81         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       74.07        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1.71        24.33         1.94        27.39        36.39        15.58 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
       35.64        35.70        17.88        17.06        40.21        22.49 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       27.02        33.11        27.91        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        3.81        19.59         7.76        66.51        13.38        11.77 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       11.61         9.73        14.20         9.99        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
        0.39         0.39        28.34         5.46         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
       28.96         0.10         2.04         0.62         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.99         1.45         1.32         0.85         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 
       17.49         3.48        26.89        17.00        14.07         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
       16.77         1.81        22.75        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       15.81        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         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-60-2696 TCGA-60-2697 
       56.65        35.24        29.92        21.11         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       66.54        41.42         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 
       48.49        42.64         3.19        32.32        23.57        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ 
       11.77       102.67        70.62        66.61        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-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       16.37        25.41        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-66-2758 TCGA-66-2759 TCGA-66-2763 
        0.92         0.99        43.99        21.01        25.05         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-66-2777 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-66-2786 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-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         5.03        30.02        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-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
       14.73        29.56        73.12        75.09        23.28        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       20.78         0.49        42.28        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        15.75        53.95        37.81        82.92        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         9.63        54.41        35.90         0.33       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB 
      132.36       117.57        22.29         5.92        42.41        30.81 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 
       27.62        38.86         9.67        12.99        34.95        31.30 
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-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       19.04        24.13        31.56        14.07        16.87        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        14.63        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC 
       12.59         0.10        15.62        25.68        19.33        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       24.36        18.18        19.73        16.21        15.85        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        0.79        12.39         3.65        24.92         9.50         2.93 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       11.77        14.07        22.62        10.59         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        4.01         5.26         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 
        4.01         5.03        26.63        16.14        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       18.31        17.46        19.36        16.57         8.42         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
       30.81        30.67        21.34         3.88        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 
       27.02        21.21        20.32        18.58        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       16.11        13.18        13.41         0.07        64.08         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       51.78         1.22        45.37        13.74         4.21         2.89 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR 
       39.85        37.22        30.58        24.00        14.73        29.75 
TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N 
       22.78        65.49         3.65        16.80         0.43        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             174.08 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            18.380             19.165 
[1] "0.4 - 133.7 (18.4)" "0.0 - 174.1 (19.2)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         1        7       19        1         3        10
  12Q LOSS WILD-TYPE       1       80      132        1        60        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  12Q LOSS MUTATED           0          5          0        0
  12Q LOSS WILD-TYPE         3         57         21        7
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  7                 80
  STAGE IB                 19                132
  STAGE II                  1                  1
  STAGE IIA                 3                 60
  STAGE IIB                10                 82
  STAGE III                 0                  3
  STAGE IIIA                5                 57
  STAGE IIIB                0                 21
  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    11  26  10   0
  12Q LOSS WILD-TYPE 100 264  59  23
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               11                100
  T2               26                264
  T3               10                 59
  T4                0                 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    35   8   3   0
  12Q LOSS WILD-TYPE 277 123  36   5
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               35                277
  N1                8                123
  N2                3                 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    37   0
  12Q LOSS WILD-TYPE 367   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     37    0
  12Q LOSS WILD-TYPE  367    7
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               37                367
  1                0                  7
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    13  34
  12Q LOSS WILD-TYPE 114 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     13   34
  12Q LOSS WILD-TYPE  114  332
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               13                114
  MALE                 34                332
[1] 2 2
[1] FALSE
D65V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED                                       2
  12Q LOSS WILD-TYPE                                    13
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED                                         0
  12Q LOSS WILD-TYPE                                       1
                    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                                                         427
D65V9, multiclass
                                                             clus
vv                                                            12Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  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 CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                427
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  46
  12Q LOSS WILD-TYPE  12 434
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   46
  12Q LOSS WILD-TYPE   12  434
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 1                 12
  YES               46                434
[1] 2 2
[1] FALSE
D65V11, continuous
D65V12, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    33   0   0   2
  12Q LOSS WILD-TYPE 361  12   4  20
D65V13, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               33                361
  R1                0                 12
  R2                0                  4
  RX                2                 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                         5    30
  12Q LOSS WILD-TYPE     7                        26   310
D65V14, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                5                 26
  WHITE                                   30                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"
D65V15, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  35
  12Q LOSS WILD-TYPE   8 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   35
  12Q LOSS WILD-TYPE    8  274
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               35                274
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   180 117
  13Q LOSS WILD-TYPE 101  79
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               297                180 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               117                 79 
$`13Q LOSS MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 
       79.46         4.80        92.15        31.99         1.64        86.96 
TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        6.18       154.32       119.54        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
       60.89       122.43        43.23        33.93        10.82        32.19 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
       21.99         4.31         1.74        27.02        48.82        20.48 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       35.08         0.56        34.75        13.12        32.02        19.30 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
       11.77        31.73        64.93        63.55        44.25         0.79 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
       79.20        11.74        18.84        30.12        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       22.06        98.01       103.53       151.27        14.07        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
        1.55        19.76        27.02         4.70         0.30        36.62 
TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       44.19         2.63        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       31.27        65.23        67.79        18.15         4.96         1.12 
TCGA-34-8456 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
       26.43         0.39         6.58         7.46         7.82         6.81 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 TCGA-39-5028 TCGA-39-5029 
        3.39        47.80        74.07        55.20         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
        1.94        27.39        35.64        22.49        38.66        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 
       33.11        18.38        12.36        24.89        21.47        19.59 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-46-6025 TCGA-51-4079 
       66.51        13.38        11.77        11.61        10.65         0.39 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-6546 
       28.34         5.46         8.75        27.45        28.96         0.62 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8307 
        0.43         1.45         0.85         6.51         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
       17.00        14.07         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       15.81        20.94        17.85         2.76         0.03        13.25 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M 
       29.95        71.24        34.78        85.12        34.36        35.24 
TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
        3.58        96.82        37.94        92.71        21.93        80.45 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
       66.54        41.42         9.01        56.91        50.33        42.64 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        3.19        32.32        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ 
       11.77       102.67        70.62        66.61        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU 
       45.57        11.34        25.28        89.29        78.28        25.41 
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-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7139 
        8.02        13.35        16.18        29.56        75.09        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
       20.78         0.49        70.13       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       15.75         6.51        53.95        82.92        12.59        53.92 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
       17.72       104.09        26.40        27.39         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       65.49        35.90       132.36       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 
       42.41        42.08        27.62         9.67        12.99        34.95 
TCGA-85-7698 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 
       31.30        29.95        18.94        19.04        31.56        14.07 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
       10.09         0.76        13.22        16.77         5.29         3.09 
TCGA-85-8580 TCGA-85-8664 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QR TCGA-85-A50Z 
       14.63         0.10        19.33        17.72        19.73        16.21 
TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
       15.85        12.39         3.65         9.50         2.93        11.77 
TCGA-90-7964 TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       14.07        22.62         2.70         3.48         4.01         5.26 
TCGA-94-7557 TCGA-94-8035 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 
        0.16         4.01        26.63        16.14        17.69        49.87 
TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       57.07        18.31        19.36         8.42        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I 
       21.34        27.16         3.88        18.15         2.01        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HD TCGA-NC-A5HE 
       20.71        19.10        12.89        16.11         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54        51.78        45.37        13.74         4.21         2.89 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
       39.85        37.22        30.58        24.00        14.73        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S 
       83.57        65.49         3.65        16.80         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

$`13Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20         7.46        75.75       117.57        11.34        23.54 
TCGA-18-3417 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1077 TCGA-21-1078 
       36.07         2.79        49.94        27.19        34.78        15.58 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
       31.73         9.34       119.80        31.63        88.11        41.69 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 
        7.33        14.93        64.21        14.10        48.33        24.13 
TCGA-22-4599 TCGA-22-4609 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5489 
       38.17         9.57        14.63        54.28        71.34        62.86 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-AASB TCGA-33-AASD 
        7.63       133.74        79.53       174.08         6.94       110.99 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
      118.36        27.16        56.38         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 
       16.93        30.94        27.19         4.04        20.91         3.95 
TCGA-37-3789 TCGA-37-4130 TCGA-37-4141 TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 
        0.43         8.12         0.39        44.75        68.58        70.03 
TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
       60.79        36.39        15.58        35.70        17.88        17.06 
TCGA-43-2576 TCGA-43-5670 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-8118 
       40.21        27.91         5.46         3.81         7.76         2.93 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4080 
        9.73        14.20        12.03         9.99        13.91         0.39 
TCGA-51-4081 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 
       29.95        30.35         0.10        18.25         2.04         0.99 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 
        0.99         1.32         0.10        17.49         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK 
        1.81        22.75        19.23        13.32        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8392 TCGA-58-A46L TCGA-58-A46N 
        0.13         0.26        13.55        16.47        56.65        29.92 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2709 TCGA-60-2715 TCGA-60-2716 
       21.11        12.23        10.22        49.48        35.34        48.49 
TCGA-63-A5MM TCGA-63-A5MT TCGA-63-A5MV TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       14.99        16.37        36.16         2.01        21.07         0.99 
TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 
       43.99         2.01         1.02         7.07        23.01         3.02 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-A59J 
        4.04         5.03        10.06        54.08         4.01        14.73 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-8008 TCGA-77-8128 
       73.12        23.28        11.18        42.28        86.76        37.81 
TCGA-77-8136 TCGA-77-8140 TCGA-77-8145 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5GB 
       39.09        11.54         6.97         0.33       126.18        30.81 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7710 
       38.86        11.97         6.41        36.53        32.91         1.38 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8350 
        1.15        25.15        24.13        16.87        34.52        22.45 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 
       32.71         2.01         0.72         7.76        13.94        12.59 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       15.62        25.68        14.96        24.36        18.18        12.56 
TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-8065 
       14.96         0.79        24.92        20.22        10.59         2.30 
TCGA-94-7033 TCGA-94-7943 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-8170 TCGA-96-A4JL 
       21.04        11.70         5.03        14.14        17.46        16.57 
TCGA-98-8020 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-LA-A446 TCGA-LA-A7SW 
        2.76        27.02        21.21        20.32        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52W 
       11.84         1.22        29.75         0.43        33.07         8.58 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.03               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            154.32             174.08 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             20.78              16.67 
[1] "0.0 - 154.3 (20.8)" "0.1 - 174.1 (16.7)"
[1] "hr=" "1.3"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         0       51       92        2        43        61
  13Q LOSS WILD-TYPE       2       36       59        0        20        31
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  13Q LOSS MUTATED           3         41         10        3
  13Q LOSS WILD-TYPE         0         21         11        4
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 51                 36
  STAGE IB                 92                 59
  STAGE II                  2                  0
  STAGE IIA                43                 20
  STAGE IIB                61                 31
  STAGE III                 3                  0
  STAGE IIIA               41                 21
  STAGE IIIB               10                 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    67 188  42  11
  13Q LOSS WILD-TYPE  44 102  27  12
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               67                 44
  T2              188                102
  T3               42                 27
  T4               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                  N0  N1  N2  N3
  13Q LOSS MUTATED   189  89  24   3
  13Q LOSS WILD-TYPE 123  42  15   2
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0              189                123
  N1               89                 42
  N2               24                 15
  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   256   3
  13Q LOSS WILD-TYPE 148   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    256    3
  13Q LOSS WILD-TYPE  148    4
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0              256                148
  1                3                  4
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    79 229
  13Q LOSS WILD-TYPE  48 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     79  229
  13Q LOSS WILD-TYPE   48  137
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               79                 48
  MALE                229                137
[1] 2 2
[1] FALSE
D66V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                       7
  13Q LOSS WILD-TYPE                                     8
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                         0
  13Q LOSS WILD-TYPE                                       1
                    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                                                           300
  13Q LOSS WILD-TYPE                                                         170
D66V9, multiclass
                                                             clus
vv                                                            13Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              300
                                                             clus
vv                                                            13Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8 300
  13Q LOSS WILD-TYPE   5 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8  300
  13Q LOSS WILD-TYPE    5  180
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                  5
  YES              300                180
[1] 2 2
[1] FALSE
D66V11, continuous
D66V12, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED   245   7   3  15
  13Q LOSS WILD-TYPE 149   5   1   7
D66V13, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0              245                149
  R1                7                  5
  R2                3                  1
  RX               15                  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   212
  13Q LOSS WILD-TYPE     7                        13   128
D66V14, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               18                 13
  WHITE                                  212                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"
D66V15, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8 180
  13Q LOSS WILD-TYPE   0 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8  180
  13Q LOSS WILD-TYPE    0  129
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  0
  NOT HISPANIC OR LATINO              180                129
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    89  67
  14Q LOSS WILD-TYPE 192 129
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               156                321 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                67                129 
$`14Q LOSS MUTATED`
TCGA-18-3410 TCGA-18-4083 TCGA-18-4086 TCGA-21-1071 TCGA-21-1083 TCGA-21-5784 
        4.80         6.18         2.79        46.88        43.23        41.69 
TCGA-22-0940 TCGA-22-1012 TCGA-22-1016 TCGA-22-4596 TCGA-22-4613 TCGA-22-5473 
       21.99        14.10        27.02         0.56        11.77        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5491 
       14.63        44.25        71.34        79.20        18.84        56.32 
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-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-5927 TCGA-34-5928 
        2.63        61.61        31.50        28.96        30.94        18.15 
TCGA-34-5929 TCGA-34-A5IX TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-39-5016 
        4.96        20.91         8.12         7.82         6.81        74.07 
TCGA-39-5021 TCGA-39-5024 TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 TCGA-43-3394 
       68.58        70.03         1.94        15.58        17.06        27.02 
TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-A475 
       21.47        19.59         7.76        66.51        11.77         9.73 
TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 TCGA-56-5897 TCGA-56-7582 
        9.99        13.91         0.39         5.46         0.10         0.85 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-A4BY TCGA-58-8387 TCGA-58-8388 
       26.89        14.07         1.35        17.85        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46K TCGA-60-2695 TCGA-60-2704 
       29.95        71.24        85.12        34.36        21.11        37.94 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2723 
       49.48        66.54         9.01        56.91        50.33        35.90 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5ML TCGA-63-A5MP 
       26.83        11.77       102.67        66.61        45.57        25.28 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
       53.88        16.96         1.02         2.01         0.92        43.99 
TCGA-66-2758 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2786 TCGA-66-2787 
       21.01         7.07        23.01         3.02        25.97        40.01 
TCGA-66-2795 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 
        4.01         6.94         8.02        13.35        14.73        29.56 
TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 
       73.12        89.98         0.49         0.16        15.75        86.76 
TCGA-77-8009 TCGA-77-8140 TCGA-77-8156 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH 
       53.95        11.54         0.33         5.92        27.62        38.86 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       11.97         6.41         1.15        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 
       19.04        24.13        31.56        16.87        10.09         0.76 
TCGA-85-8288 TCGA-85-8352 TCGA-85-8580 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN 
       13.22         5.29        14.63         0.10        25.68        19.33 
TCGA-85-A4JC TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-90-7766 TCGA-90-7767 
       14.96        15.85        14.96         0.79         9.50         2.93 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-94-7557 TCGA-94-7943 
       11.77        20.22        22.62        10.59         0.16        11.70 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       16.14        17.69        57.07        16.57         8.42        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53J TCGA-LA-A446 TCGA-NC-A5HD 
       30.67        21.34        18.15        20.71        13.18         0.07 
TCGA-NC-A5HE TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NK-A5CT TCGA-XC-AA0X 
       64.08        13.74         4.21         2.89        65.49         0.20 

$`14Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       23.54        92.15        31.99        36.07         1.64        86.96 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 
      154.32        49.94        27.19       119.54        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-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
      119.80        31.63        88.11        33.93        10.82        32.19 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1017 
        7.33        14.93         4.31        64.21         1.74        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
       20.48        35.08        48.33        24.13        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 
       13.12        32.02        19.30         9.57        31.73        64.93 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 
        0.79        54.28        11.74        30.12        62.86        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       22.06         7.63       133.74        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASB TCGA-33-AASD 
      103.53         1.55        19.76        27.02         6.94       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
       44.19       118.36        27.16        32.88        31.27        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       67.79        56.38         9.07        23.24        12.00        16.93 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 
        1.12        27.19         4.04        26.43         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        0.39         6.58         7.46         0.39         3.39        47.80 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 
       44.75        55.20        60.79         1.71        24.33        27.39 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 
       36.39        35.64        35.70        17.88        40.21        22.49 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       38.66        33.11        18.38        27.91        12.36        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U 
        5.46         3.81        13.38         2.93        11.61        14.20 
TCGA-43-A56V TCGA-46-6025 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 
       12.03        10.65         0.39        29.95        28.34        30.35 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        8.75        27.45        28.96        18.25         2.04         0.62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 
        0.99         0.43         0.99         1.45         1.32         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8504 TCGA-56-8622 
        0.10        17.49         3.48        17.00        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       20.94        19.23        13.32        21.04        18.74         0.13 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L 
        0.26         2.76         0.03        16.47        34.78        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       35.24        29.92         3.58        12.23        10.22        96.82 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 
       92.71        21.93        80.45        41.42        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-63-A5MG 
       42.64         3.19        32.32        29.85        23.57        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-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 
       16.37        25.41        36.16        34.59        43.10         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
       21.07         0.99         0.99        25.05         0.99         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 
        1.02         2.01         2.01        19.00         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
       12.03         3.98        12.00        24.95         1.97        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-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I TCGA-77-6844 TCGA-77-6845 
       49.05         2.73         6.64        16.18        75.09        23.28 
TCGA-77-7138 TCGA-77-7140 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
       11.18        20.78        42.28        70.13       106.95        46.78 
TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        6.51        37.81        82.92        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       17.72       104.09        26.40        27.39         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       54.41        65.49        35.90       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6175 TCGA-85-6561 
       22.29        42.41        42.08        30.81         9.67        12.99 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-8071 
       36.53        34.95        31.30        32.91         1.38        14.07 
TCGA-85-8276 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       34.52        22.45        16.77         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4JB 
        0.72         7.76        13.94        12.59        15.62        17.72 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A53L 
       24.36        18.18        19.73        12.56        16.21        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7964 TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
        3.65        24.92        14.07         2.70         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        5.26         2.30        21.04         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8020 
       14.14        49.87        18.31        17.46        19.36         2.76 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       27.16         3.88         2.01        27.02        21.21        20.32 
TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 
       18.58        19.10        12.89        16.11        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HM TCGA-NC-A5HN 
        4.54        51.78         1.22        45.37        39.85        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       30.58        24.00        14.73        29.75        22.78        83.57 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
        3.65        16.80         0.43        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       43.89         8.58        11.18 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            151.27             174.08 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             17.01              20.48 
[1] "0.1 - 151.3 (17.0)" "0.0 - 174.1 (20.5)"
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         0       36       53        0        23        31
  14Q LOSS WILD-TYPE       2       51       98        2        40        61
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  14Q LOSS MUTATED           0         13          5        0
  14Q LOSS WILD-TYPE         3         49         16        7
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 36                 51
  STAGE IB                 53                 98
  STAGE II                  0                  2
  STAGE IIA                23                 40
  STAGE IIB                31                 61
  STAGE III                 0                  3
  STAGE IIIA               13                 49
  STAGE IIIB                5                 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
  14Q LOSS MUTATED    47  94  16   4
  14Q LOSS WILD-TYPE  64 196  53  19
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               47                 64
  T2               94                196
  T3               16                 53
  T4                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                  N0  N1  N2  N3
  14Q LOSS MUTATED   105  47   7   0
  14Q LOSS WILD-TYPE 207  84  32   5
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              105                207
  N1               47                 84
  N2                7                 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   136   0
  14Q LOSS WILD-TYPE 268   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    136    0
  14Q LOSS WILD-TYPE  268    7
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              136                268
  1                0                  7
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    44 117
  14Q LOSS WILD-TYPE  83 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     44  117
  14Q LOSS WILD-TYPE   83  249
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               44                 83
  MALE                117                249
[1] 2 2
[1] FALSE
D67V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED                                       5
  14Q LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED                                         0
  14Q LOSS WILD-TYPE                                       1
                    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                                                           155
  14Q LOSS WILD-TYPE                                                         315
D67V9, multiclass
                                                             clus
vv                                                            14Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              155
                                                             clus
vv                                                            14Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                315
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     4 157
  14Q LOSS WILD-TYPE   9 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4  157
  14Q LOSS WILD-TYPE    9  323
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 4                  9
  YES              157                323
[1] 2 2
[1] FALSE
D67V11, continuous
D67V12, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED   133   3   1   5
  14Q LOSS WILD-TYPE 261   9   3  17
D67V13, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0              133                261
  R1                3                  9
  R2                1                  3
  RX                5                 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
  14Q LOSS MUTATED       3                         9   119
  14Q LOSS WILD-TYPE     6                        22   221
D67V14, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                9                 22
  WHITE                                  119                221
[1] 3 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     1 108
  14Q LOSS WILD-TYPE   7 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1  108
  14Q LOSS WILD-TYPE    7  201
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO              108                201
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    78  59
  15Q LOSS WILD-TYPE 203 137
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               137                340 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                59                137 
$`15Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3412 TCGA-18-3416 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       12.20        11.34        31.99        49.94       119.54        46.88 
TCGA-21-1072 TCGA-21-1080 TCGA-21-5787 TCGA-22-0944 TCGA-22-1000 TCGA-22-1012 
       99.16       122.43        10.82         7.33        14.93        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       27.02        48.82        48.33        24.13         0.56        38.17 
TCGA-22-5471 TCGA-22-5480 TCGA-33-4533 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 
       31.73        71.34       133.74       103.53        54.44         1.55 
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         3.95         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 
       47.80        74.07        68.58         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 
       27.39        36.39        17.06        22.49        38.66        18.38 
TCGA-43-5670 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-52-7810 
       27.91        12.03         9.99        10.65        13.91        30.35 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7822 TCGA-56-8304 TCGA-56-8309 TCGA-56-8503 
        0.99         1.32        17.49         3.48        14.07         1.35 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A62T TCGA-58-8386 TCGA-60-2698 TCGA-60-2703 
       20.94        19.23         2.76         0.03        10.22        96.82 
TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 TCGA-60-2720 TCGA-60-2723 TCGA-60-2726 
       80.45         9.01        50.33         3.19        35.90        11.77 
TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-63-A5MW 
      102.67        66.61        59.97        45.57        78.28        53.88 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2756 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 
        2.01        21.07         0.99         5.03        10.06        54.08 
TCGA-66-2800 TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-7139 
       49.05         8.02        16.18        14.73        29.56        89.98 
TCGA-77-7337 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8145 
      106.95         6.51        53.95        37.81        82.92         6.97 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       65.49         0.33        22.29        38.86         9.67        11.97 
TCGA-85-7696 TCGA-85-7843 TCGA-85-8072 TCGA-85-8288 TCGA-85-8479 TCGA-85-8666 
       36.53         1.15        16.87        13.22         0.72        15.62 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 
       18.18        12.56        14.96        12.39         3.65         2.93 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 TCGA-94-8491 TCGA-96-A4JK 
       20.22        22.62         5.26         2.30        26.63        19.36 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK 
       11.84         0.07         4.54        51.78        45.37         4.21 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR 
        2.89        39.85        37.22        24.00        14.73        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52W TCGA-O2-A5IB 
        3.65        33.07         3.72         8.58        11.18 

$`15Q LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
        7.46        75.75        79.46         4.80       117.57        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       92.15        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
      154.32        27.19        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-21-A5DI TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 
       41.69        33.93        32.19        21.99         4.31        64.21 
TCGA-22-1011 TCGA-22-4591 TCGA-22-4593 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
        1.74        20.48        35.08        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
       19.30         9.57        11.77        64.93        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       44.25         0.79        54.28        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
       30.12        62.86        56.32        16.64        22.06         7.63 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-6737 
       98.01        79.53       174.08       151.27        14.07        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASL TCGA-34-2596 
       27.02         4.70         0.30         6.94        27.16         2.63 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
       31.50        28.96        32.88        31.27        65.23        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       56.38         9.07        23.24        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 
       18.15         1.12        27.19         4.04        20.91         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-39-5019 TCGA-39-5022 
        0.39         6.58         7.46         6.81        44.75        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
       70.03        60.79        15.58        35.64        35.70        17.88 
TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       40.21        27.02        33.11        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
        5.46         3.81        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 
       11.77         2.93        11.61         9.73        14.20         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-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
       28.96         0.10        18.25         2.04         0.62         0.99 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8307 
        0.43         1.45         0.85         6.51         0.10        26.89 
TCGA-56-8308 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       17.00        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
        9.93        20.25        15.81        13.32        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       18.74         0.13         0.26        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-60-2696 TCGA-60-2697 TCGA-60-2704 
       35.24        29.92        21.11         3.58        12.23        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
       92.71        21.93        49.48        66.54        41.42        56.91 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 
       35.34        48.49        42.64        32.32        29.85        23.57 
TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       26.83        70.62        58.65        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 
       89.29        16.37        25.41        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-77-6843 
        4.01         2.73         6.64         6.94        13.35        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       75.09        23.28        11.18        20.78         0.49        42.28 
TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8131 
       70.13         0.16        46.78        15.75        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         9.63        54.41        35.90       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
      117.57         5.92        42.41        42.08        30.81        27.62 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
       12.99         6.41        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-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 
       14.07        34.52        10.09         0.76        22.45        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        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       13.94        12.59         0.10        25.68        19.33        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 
       14.96        24.36        19.73        16.21        15.85         0.79 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 
       24.92         9.50        11.77        14.07        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 
        3.48         4.01        21.04         0.16        11.70         4.01 
TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
        5.03        14.14        16.14        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 
       18.31        17.46        16.57         8.42         2.76        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
       30.67        21.34        27.16         3.88        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       27.02        21.21        20.32        18.58        20.71        19.10 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HE TCGA-NC-A5HH 
       12.89        16.11        13.18        13.41        64.08         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HO TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5D1 
       13.74        30.58        29.75        22.78        65.49        16.80 
TCGA-NK-A7XE TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
        0.43        12.72        43.89         0.20 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.03               0.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            133.74             174.08 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             18.38              19.20 
[1] "0.0 - 133.7 (18.4)" "0.1 - 174.1 (19.2)"
[1] "hr=" "1"  
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         2       20       36        0        18        30
  15Q LOSS WILD-TYPE       0       67      115        2        45        62
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  15Q LOSS MUTATED           2         21          8        3
  15Q LOSS WILD-TYPE         1         41         13        4
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 20                 67
  STAGE IB                 36                115
  STAGE II                  0                  2
  STAGE IIA                18                 45
  STAGE IIB                30                 62
  STAGE III                 2                  1
  STAGE IIIA               21                 41
  STAGE IIIB                8                 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
  15Q LOSS MUTATED    26  85  21   8
  15Q LOSS WILD-TYPE  85 205  48  15
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               26                 85
  T2               85                205
  T3               21                 48
  T4                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                  N0  N1  N2  N3
  15Q LOSS MUTATED    78  45  15   1
  15Q LOSS WILD-TYPE 234  86  24   4
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               78                234
  N1               45                 86
  N2               15                 24
  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 293   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    111    3
  15Q LOSS WILD-TYPE  293    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              111                293
  1                3                  4
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    39 101
  15Q LOSS WILD-TYPE  88 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     39  101
  15Q LOSS WILD-TYPE   88  265
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               39                 88
  MALE                101                265
[1] 2 2
[1] FALSE
D68V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED                                       2
  15Q LOSS WILD-TYPE                                    13
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED                                         0
  15Q LOSS WILD-TYPE                                       1
                    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                                                           136
  15Q LOSS WILD-TYPE                                                         334
D68V9, multiclass
                                                             clus
vv                                                            15Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              136
                                                             clus
vv                                                            15Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                334
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     6 134
  15Q LOSS WILD-TYPE   7 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6  134
  15Q LOSS WILD-TYPE    7  346
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 6                  7
  YES              134                346
[1] 2 2
[1] FALSE
D68V11, continuous
D68V12, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED   112   3   2   5
  15Q LOSS WILD-TYPE 282   9   2  17
D68V13, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              112                282
  R1                3                  9
  R2                2                  2
  RX                5                 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 LOSS MUTATED       4                        13    93
  15Q LOSS WILD-TYPE     5                        18   247
D68V14, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN               13                 18
  WHITE                                   93                247
[1] 3 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  85
  15Q LOSS WILD-TYPE   6 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   85
  15Q LOSS WILD-TYPE    6  224
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               85                224
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    96  59
  16P LOSS WILD-TYPE 185 137
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               155                322 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                59                137 
$`16P LOSS MUTATED`
TCGA-18-3410 TCGA-18-3415 TCGA-18-4083 TCGA-18-5592 TCGA-21-1070 TCGA-21-1076 
        4.80        92.15         6.18        49.94       119.54        60.89 
TCGA-21-1080 TCGA-21-5786 TCGA-22-0940 TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 
      122.43        33.93        21.99         4.31        14.10        48.33 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 
       24.13        38.17        13.12        11.77         0.79        71.34 
TCGA-22-5482 TCGA-33-4533 TCGA-33-6737 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ 
       11.74       133.74        19.76         6.94        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2609 TCGA-34-5236 TCGA-34-5239 TCGA-34-5927 
       27.16         2.63        31.27         9.07        23.24        30.94 
TCGA-34-5928 TCGA-34-8455 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 
       18.15         4.04        47.80        74.07        68.58        60.79 
TCGA-39-5028 TCGA-39-5040 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 
        1.71        17.06        27.02        27.91        12.36        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-A56U TCGA-46-6025 TCGA-52-7622 
        7.76        66.51        11.77        14.20        10.65        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8629 
        5.46        30.35         1.32        17.49         1.35        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-58-8386 TCGA-58-8391 TCGA-58-8392 
       20.94        13.32        17.85         0.03        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-A5MB 
       50.33        42.64         3.19        35.90        23.57       102.67 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MY TCGA-66-2727 
       66.61        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-66-2763 
       43.10         1.02         0.92        43.99        21.01         0.99 
TCGA-66-2769 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        7.07         3.98        12.00         1.97        25.97        40.01 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-77-6842 
       22.98        30.02        49.05         6.64        13.35        29.56 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7463 TCGA-77-8130 TCGA-77-8136 TCGA-77-8140 
       89.98        42.28        46.78        82.92        39.09        11.54 
TCGA-77-8143 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH 
       26.40        35.90         0.33         5.92        27.62        38.86 
TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 
        6.41        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        14.63 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A53L 
        0.10        15.62        19.33        14.96        19.73        12.39 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-92-8064 TCGA-94-7557 TCGA-94-8035 
        3.65         2.93        22.62         5.26         0.16         4.01 
TCGA-96-7544 TCGA-96-8169 TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53A TCGA-98-A53I 
       49.87        18.31        19.36         3.88        18.15        18.58 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HG TCGA-NC-A5HJ 
       12.89        16.11        13.41         0.07        51.78        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
        4.21         2.89        37.22        29.75        22.78        83.57 
TCGA-NK-A5CT TCGA-O2-A52N TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       65.49        33.07         8.58        11.18         0.20 

$`16P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       23.54        31.99        36.07         1.64        86.96         2.79 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 
      154.32        27.19        46.88        99.16        70.16        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-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 
       88.11        41.69        10.82        32.19         7.33        14.93 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
       64.21         1.74        27.02        48.82        20.48        35.08 
TCGA-22-4596 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 
        0.56        34.75        32.02        19.30         9.57        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5481 
       64.93        63.55        14.63        44.25        54.28        79.20 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       18.84        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        7.63        98.01        79.53       174.08       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       14.07        54.44         1.55        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       36.62       110.99        61.61        31.50        28.96        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5929 
       65.23        67.79        56.38        12.00        16.93         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        1.12        27.19        26.43        20.91         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.39         6.58         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 
        0.39         3.39        44.75        55.20        70.03        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        27.39        36.39        15.58        35.64        35.70 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 
       17.88        40.21        22.49        38.66        33.11        18.38 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-8118 
       24.89        21.47         5.46         3.81        13.38         2.93 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 
       11.61         9.73        12.03         9.99        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        0.39        29.95         8.75        27.45        28.96         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
       18.25         2.04         0.62         0.99         0.43         0.99 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        1.45         0.85         6.51         0.10         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       17.00        14.07        16.77         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK 
       10.36         9.93        20.25        19.23        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.13         0.26         2.76        13.25        13.55        29.95 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       35.24        29.92         3.58        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       37.94        92.71        21.93        49.48        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 TCGA-60-2722 
        9.01        56.91        35.34        48.49        32.32        29.85 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN 
       26.83        11.77        70.62        59.97        14.99        11.34 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       89.29        78.28        16.37        25.41        36.16        53.88 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 TCGA-66-2759 
        2.01        21.07         0.99         2.01         0.99        25.05 
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-66-2783 TCGA-66-2788 
        3.02         2.01        19.00        12.03        24.95        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 
        4.04         5.03        10.06        54.08         4.01         2.73 
TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 
        6.94         8.02        16.18        14.73        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       23.28        11.18        20.78         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        15.75         6.51        86.76        53.95        37.81 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 
       12.59        53.92        17.72       104.09        27.39         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        9.63        54.41        65.49       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6175 TCGA-85-6560 
       22.29        42.41        42.08        30.81         9.67        11.97 
TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       12.99        36.53        34.95         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        14.07        16.87        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         0.72         7.76        13.94 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       12.59        25.68        17.72        24.36        18.18        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 
       16.21        15.85        14.96         0.79        24.92         9.50 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       11.77        14.07        20.22        10.59         2.70         3.48 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-8490 TCGA-94-8491 
        4.01         2.30        21.04        11.70         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL 
       14.14        16.14        17.69        57.07        17.46        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
        8.42         2.76        30.81        30.67        21.34        27.16 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-J1-A4AH 
        2.01        27.02        21.21        20.32        20.71        19.10 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI 
       13.18        11.84        64.08         4.54         1.22        45.37 
TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-NK-A5D1 
       39.85        30.58        24.00        14.73         3.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
        0.43         3.72        12.72        43.89 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.03               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            133.74             174.08 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             19.73              18.92 
[1] "0.0 - 133.7 (19.7)" "0.1 - 174.1 (18.9)"
[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       51        0        17        35
  16P LOSS WILD-TYPE       0       61      100        2        46        57
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  16P LOSS MUTATED           1         23          3        2
  16P LOSS WILD-TYPE         2         39         18        5
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 26                 61
  STAGE IB                 51                100
  STAGE II                  0                  2
  STAGE IIA                17                 46
  STAGE IIB                35                 57
  STAGE III                 1                  2
  STAGE IIIA               23                 39
  STAGE IIIB                3                 18
  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
  16P LOSS MUTATED    28 100  25   7
  16P LOSS WILD-TYPE  83 190  44  16
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               28                 83
  T2              100                190
  T3               25                 44
  T4                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                  N0  N1  N2  N3
  16P LOSS MUTATED   105  43  11   0
  16P LOSS WILD-TYPE 207  88  28   5
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0              105                207
  N1               43                 88
  N2               11                 28
  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   134   2
  16P LOSS WILD-TYPE 270   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    134    2
  16P LOSS WILD-TYPE  270    5
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0              134                270
  1                2                  5
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    45 115
  16P LOSS WILD-TYPE  82 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     45  115
  16P LOSS WILD-TYPE   82  251
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               45                 82
  MALE                115                251
[1] 2 2
[1] FALSE
D69V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED                                       8
  16P LOSS WILD-TYPE                                     7
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED                                         0
  16P LOSS WILD-TYPE                                       1
                    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                                                           152
  16P LOSS WILD-TYPE                                                         318
D69V9, multiclass
                                                             clus
vv                                                            16P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      8
  LUNG CLEAR CELL 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)              152
                                                             clus
vv                                                            16P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                318
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     4 156
  16P LOSS WILD-TYPE   9 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4  156
  16P LOSS WILD-TYPE    9  324
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 4                  9
  YES              156                324
[1] 2 2
[1] FALSE
D69V11, continuous
D69V12, continuous
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED   131   1   0   6
  16P LOSS WILD-TYPE 263  11   4  16
D69V13, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0              131                263
  R1                1                 11
  R2                0                  4
  RX                6                 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
  16P LOSS MUTATED       1                        15   103
  16P LOSS WILD-TYPE     8                        16   237
D69V14, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN               15                 16
  WHITE                                  103                237
[1] 3 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  96
  16P LOSS WILD-TYPE   6 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2   96
  16P LOSS WILD-TYPE    6  213
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               96                213
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   107  65
  16Q LOSS WILD-TYPE 174 131
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               172                305 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                65                131 
$`16Q LOSS MUTATED`
TCGA-18-3410 TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-5592 TCGA-21-1070 
        4.80        92.15         1.64         6.18        49.94       119.54 
TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-22-0940 TCGA-22-1002 TCGA-22-1012 
       60.89       122.43        43.23        21.99         4.31        14.10 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-5473 TCGA-22-5478 
       48.33        24.13        38.17        13.12        63.55         0.79 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 TCGA-33-4533 TCGA-33-4586 TCGA-33-6737 
       71.34        79.20        62.86       133.74        14.07        19.76 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2604 TCGA-34-2609 
       44.19       118.36        27.16         2.63        31.50        31.27 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       65.23         9.07        23.24        30.94        18.15         4.96 
TCGA-34-8455 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 
        4.04        47.80        74.07        44.75        60.79         1.71 
TCGA-39-5030 TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
        1.94        17.06        22.49        27.02        33.11        27.91 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 
        7.76        66.51        11.77        14.20        10.65        13.91 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-7221 TCGA-56-7222 TCGA-56-7580 
       28.34         5.46        30.35         0.99         0.43         1.32 
TCGA-56-7730 TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8626 
        6.51        17.49        26.89        14.07         1.35         9.93 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       20.94        13.32        17.85         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-60-2695 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
       35.24        21.11        66.54        41.42        56.91        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI 
       42.64         3.19        35.90       102.67        66.61        58.65 
TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 
       45.57        25.28        34.59        16.96        43.10         1.02 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 
        0.92        43.99        21.01        25.05         0.99         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2778 TCGA-66-2782 TCGA-66-2787 TCGA-66-2789 
        7.07        23.01        19.00        12.00        40.01         4.04 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 
       22.98        30.02        10.06        49.05         6.64        13.35 
TCGA-68-A59J TCGA-77-6842 TCGA-77-7139 TCGA-77-7142 TCGA-77-7463 TCGA-77-8136 
       14.73        29.56        89.98        42.28        46.78        39.09 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
      104.09        11.54        26.40        54.41        65.49         0.33 
TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7950 
       38.86        12.99         6.41        31.30        32.91        18.94 
TCGA-85-8071 TCGA-85-8353 TCGA-85-8355 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
       14.07         3.09         2.01        14.63         0.10        15.62 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-7767 
       19.33        17.72        14.96        19.73         3.65         2.93 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 TCGA-94-7557 TCGA-94-8035 
       20.22        22.62         5.26         2.30         0.16         4.01 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-8169 TCGA-96-A4JK TCGA-98-A538 TCGA-98-A539 
       14.14        16.14        18.31        19.36        27.16         3.88 
TCGA-98-A53A TCGA-98-A53I TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN 
       18.15        18.58        51.78        13.74         2.89        37.22 
TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       30.58        14.73        29.75        22.78        83.57        65.49 
TCGA-O2-A52N TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         8.58        11.18         0.20 

$`16Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       23.54        31.99        36.07        86.96         2.79       154.32 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
       27.19        46.88        99.16        70.16        34.78        15.58 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
       31.73         9.34       119.80        31.63        88.11        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 
       33.93        10.82        32.19         7.33        14.93        64.21 
TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 
        1.74        27.02        48.82        20.48        35.08         0.56 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       34.75        32.02        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 
       64.93        14.63        44.25        54.28        11.74        18.84 
TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
       30.12        56.32        16.64        22.06         7.63        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 
       79.53       174.08       103.53       151.27        54.44         1.55 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       27.02         4.70         0.30        36.62         6.94       110.99 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 
       61.61        28.96        32.88        67.79        56.38        12.00 
TCGA-34-5241 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
       16.93         1.12        27.19        26.43        20.91         3.95 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         6.58         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        6.81         0.39         3.39        68.58        55.20        70.03 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
       24.33        27.39        36.39        15.58        35.64        35.70 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 
       17.88        40.21        38.66        18.38        12.36        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8118 
       21.47         5.46         3.81        19.59        13.38         2.93 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 TCGA-51-4079 TCGA-51-4080 
       11.61         9.73        12.03         9.99         0.39         0.39 
TCGA-51-4081 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       29.95         8.75        27.45        28.96         0.10        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 
        2.04         0.62         0.99         1.45         0.85         0.10 
TCGA-56-8304 TCGA-56-8308 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
        3.48        17.00        16.77         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK 
       10.36        20.25        15.81        19.23        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-A46K TCGA-58-A46N TCGA-60-2696 
        0.13         0.26         2.76        34.36        29.92         3.58 
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-60-2712 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 
       80.45        49.48         9.01        35.34        48.49        32.32 
TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MJ 
       29.85        23.57        26.83        11.77        70.62        59.97 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       14.99        11.34        89.29        78.28        16.37        25.41 
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-68-8250 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
        8.02        16.18        73.12        75.09        23.28        11.18 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 
       20.78         0.49        70.13       106.95         0.16        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        6.51        86.76        53.95        37.81        82.92        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         9.63        35.90 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       117.57        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 
       42.08        30.81        27.62         9.67        11.97        36.53 
TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 
       34.95         1.38         1.15        29.95        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        16.87        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         0.72 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ 
        7.76        13.94        12.59        25.68        24.36        18.18 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       12.56        16.21        15.85        14.96         0.79        12.39 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 
       24.92         9.50        11.77        14.07        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-94-7033 TCGA-94-7943 TCGA-94-8490 TCGA-94-8491 
        3.48         4.01        21.04        11.70         5.03        26.63 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       17.69        49.87        57.07        17.46        16.57         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53B TCGA-98-A53C 
        2.76        30.81        30.67        21.34         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
       21.21        20.32        20.71        19.10        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       13.18        13.41        11.84         0.07        64.08         4.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HP TCGA-NK-A5CX 
        1.22        45.37         4.21        39.85        24.00         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       16.80         0.43         3.72        12.72        43.89 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.03               0.07 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            133.74             174.08 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             20.58              18.38 
[1] "0.0 - 133.7 (20.6)" "0.1 - 174.1 (18.4)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         2       29       55        0        20        36
  16Q LOSS WILD-TYPE       0       58       96        2        43        56
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  16Q LOSS MUTATED           1         25          7        2
  16Q LOSS WILD-TYPE         2         37         14        5
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   2                  0
  STAGE IA                 29                 58
  STAGE IB                 55                 96
  STAGE II                  0                  2
  STAGE IIA                20                 43
  STAGE IIB                36                 56
  STAGE III                 1                  2
  STAGE IIIA               25                 37
  STAGE IIIB                7                 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
  16Q LOSS MUTATED    35 109  27   8
  16Q LOSS WILD-TYPE  76 181  42  15
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               35                 76
  T2              109                181
  T3               27                 42
  T4                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                  N0  N1  N2  N3
  16Q LOSS MUTATED   114  46  14   3
  16Q LOSS WILD-TYPE 198  85  25   2
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0              114                198
  N1               46                 85
  N2               14                 25
  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   150   2
  16Q LOSS WILD-TYPE 254   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    150    2
  16Q LOSS WILD-TYPE  254    5
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              150                254
  1                2                  5
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    54 125
  16Q LOSS WILD-TYPE  73 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     54  125
  16Q LOSS WILD-TYPE   73  241
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               54                 73
  MALE                125                241
[1] 2 2
[1] FALSE
D70V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED                                       7
  16Q LOSS WILD-TYPE                                     8
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED                                         0
  16Q LOSS WILD-TYPE                                       1
                    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                                                           172
  16Q LOSS WILD-TYPE                                                         298
D70V9, multiclass
                                                             clus
vv                                                            16Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG CLEAR CELL 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)              172
                                                             clus
vv                                                            16Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                298
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     7 172
  16Q LOSS WILD-TYPE   6 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7  172
  16Q LOSS WILD-TYPE    6  308
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 7                  6
  YES              172                308
[1] 2 2
[1] FALSE
D70V11, continuous
D70V12, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED   139   2   2   7
  16Q LOSS WILD-TYPE 255  10   2  15
D70V13, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0              139                255
  R1                2                 10
  R2                2                  2
  RX                7                 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
  16Q LOSS MUTATED       1                        13   120
  16Q LOSS WILD-TYPE     8                        18   220
D70V14, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN               13                 18
  WHITE                                  120                220
[1] 3 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     2 109
  16Q LOSS WILD-TYPE   6 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2  109
  16Q LOSS WILD-TYPE    6  200
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO              109                200
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   168 112
  17P LOSS WILD-TYPE 113  84
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               280                197 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               112                 84 
$`17P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
       12.20         7.46         4.80       117.57        23.54        92.15 
TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 TCGA-21-1075 
       31.99         1.64        86.96       154.32       119.54        70.16 
TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       34.78       122.43       119.80        43.23        31.63        88.11 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       33.93        10.82        32.19         7.33        14.93         4.31 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
        1.74        14.10        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-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
       64.93        63.55        44.25         0.79        71.34        79.20 
TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4547 
       18.84        62.86        56.32        16.64        22.06        79.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AAS8 
      151.27        14.07        54.44        27.02         0.30        36.62 
TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 
        6.94       118.36        27.16        61.61        31.50        32.88 
TCGA-34-5231 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
       65.23        27.19         4.04        26.43        20.91         3.95 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        0.43         0.39         7.82         6.81         0.39         3.39 
TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
       74.07        70.03        60.79        24.33         1.94        36.39 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 
       15.58        17.06        40.21        38.66        27.02        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
       27.91        12.36        19.59        66.51        13.38        11.77 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4080 
       11.61         9.73        14.20        12.03        13.91         0.39 
TCGA-52-7622 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       28.34        30.35        27.45        28.96         0.10        18.25 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 
        0.99         1.45         1.32        17.49         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         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
       20.25        15.81        20.94        13.32        17.85        21.04 
TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.13         2.76         0.03        13.25        13.55        29.95 
TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
       34.78        56.65        35.24        21.11         3.58        10.22 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 
       96.82        92.71        21.93        80.45        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        9.01        56.91        50.33        42.64         3.19        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       29.85        35.90        26.83        70.62        66.61        58.65 
TCGA-63-A5MJ TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       59.97        16.37        36.16        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2759 
       43.10        21.07         1.02         2.01        43.99        25.05 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
        0.99         1.02         2.01         2.01         7.07        19.00 
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-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 
        1.97        25.97        22.98         4.04         5.03        10.06 
TCGA-66-2795 TCGA-68-7757 TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
        4.01         6.94        29.56        75.09        23.28        89.98 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 
        0.49        70.13       106.95         0.16        15.75        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       53.95        37.81        82.92        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         9.63 
TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       54.41        35.90       132.36       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 
       42.41        30.81        38.86        11.97        36.53        34.95 
TCGA-85-7710 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8287 
        1.38        29.95        24.13        31.56        34.52         0.76 
TCGA-85-8288 TCGA-85-8479 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       13.22         0.72        12.59        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A513 TCGA-85-A53L 
       17.72        18.18        19.73        16.21         0.79        12.39 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7341 
        9.50         2.93        14.07        20.22        10.59         3.48 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 
        4.01         2.30        21.04         5.03        26.63        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 
       17.69        49.87        57.07        17.46        16.57        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J 
       30.67        27.16         3.88        18.15         2.01        20.71 
TCGA-L3-A4E7 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK 
       12.89         0.07         4.54        51.78        45.37         4.21 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR 
       39.85        37.22        30.58        24.00        14.73        29.75 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q 
       83.57        65.49         3.65        16.80        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89        11.18         0.20 

$`17P LOSS WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 
       75.75        79.46        11.34        36.07         6.18         2.79 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 
       49.94        27.19        46.88        99.16        60.89        15.58 
TCGA-21-1079 TCGA-21-1081 TCGA-21-5784 TCGA-22-0940 TCGA-22-1005 TCGA-22-1017 
       31.73         9.34        41.69        21.99        64.21        48.82 
TCGA-22-4593 TCGA-22-4601 TCGA-22-4613 TCGA-22-5471 TCGA-22-5474 TCGA-22-5479 
       35.08        34.75        11.77        31.73        14.63        54.28 
TCGA-22-5482 TCGA-22-5485 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
       11.74        30.12         7.63       133.74        98.01       174.08 
TCGA-33-4582 TCGA-33-4589 TCGA-33-6737 TCGA-33-A4WN TCGA-33-AASD TCGA-33-AASI 
      103.53         1.55        19.76         4.70       110.99        44.19 
TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
        2.63        28.96        31.27        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       23.24        12.00        16.93        30.94        18.15         4.96 
TCGA-34-7107 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5019 
        1.12         6.58         8.12         7.46        47.80        44.75 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5028 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 
       68.58        55.20         1.71        27.39        35.64        35.70 
TCGA-39-5039 TCGA-43-2578 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       17.88        22.49        33.11        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7657 TCGA-43-8118 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 
        3.81         7.76         2.93         9.99        10.65         0.39 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
       29.95         5.46         8.75         2.04         0.62         0.99 
TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8308 TCGA-56-8504 
        0.43         0.85         6.51         0.10        17.00        16.77 
TCGA-56-8623 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8391 TCGA-58-8392 
       22.75        19.23        18.74         0.26        71.24        16.47 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N TCGA-60-2697 TCGA-60-2704 TCGA-60-2709 
       85.12        34.36        29.92        12.23        37.94        49.48 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5ML 
       35.34        48.49        23.57        11.77       102.67        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU 
       14.99        11.34        25.28        89.29        78.28        25.41 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2765 
        2.01         0.99         0.92         0.99        21.01         2.01 
TCGA-66-2770 TCGA-66-2778 TCGA-66-2787 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 
       23.01        19.00        40.01        22.98        30.02        54.08 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
       49.05         2.73         6.64         8.02        13.35        16.18 
TCGA-68-A59J TCGA-77-6843 TCGA-77-7138 TCGA-77-7140 TCGA-77-7142 TCGA-77-7463 
       14.73        73.12        11.18        20.78        42.28        46.78 
TCGA-77-8007 TCGA-77-8143 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5GA 
        6.51        26.40        65.49         0.33       126.18        42.08 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 
       27.62         9.67        12.99         6.41        31.30        32.91 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 
        1.15        18.94        25.15        19.04        14.07        16.87 
TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       10.09        22.45        16.77         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4JC 
        2.01         7.76        14.63        13.94         0.10        14.96 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-6837 
       24.36        12.56        15.85        14.96         3.65        24.92 
TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 TCGA-92-8064 TCGA-94-7557 TCGA-94-7943 
       11.77        22.62         2.70         5.26         0.16        11.70 
TCGA-94-8035 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8020 
        4.01        14.14        18.31        19.36         8.42         2.76 
TCGA-98-8023 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH 
       21.34        27.02        21.21        20.32        18.58        19.10 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HH 
       16.11        13.18        13.41        11.84        64.08         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HT TCGA-NK-A7XE TCGA-O2-A52W 
       13.74         2.89        22.78         0.43         8.58 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            154.32             174.08 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            20.595             18.150 
[1] "0.0 - 154.3 (20.6)" "0.1 - 174.1 (18.1)"
[1] "hr=" "1.2"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         1       53       83        1        39        51
  17P LOSS WILD-TYPE       1       34       68        1        24        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  17P LOSS MUTATED           3         39         13        5
  17P LOSS WILD-TYPE         0         23          8        2
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 53                 34
  STAGE IB                 83                 68
  STAGE II                  1                  1
  STAGE IIA                39                 24
  STAGE IIB                51                 41
  STAGE III                 3                  0
  STAGE IIIA               39                 23
  STAGE IIIB               13                  8
  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    69 164  44  11
  17P LOSS WILD-TYPE  42 126  25  12
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               69                 42
  T2              164                126
  T3               44                 25
  T4               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                  N0  N1  N2  N3
  17P LOSS MUTATED   179  71  30   4
  17P LOSS WILD-TYPE 133  60   9   1
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              179                133
  N1               71                 60
  N2               30                  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   234   5
  17P LOSS WILD-TYPE 170   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    234    5
  17P LOSS WILD-TYPE  170    2
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              234                170
  1                5                  2
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    75 213
  17P LOSS WILD-TYPE  52 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     75  213
  17P LOSS WILD-TYPE   52  153
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               75                 52
  MALE                213                153
[1] 2 2
[1] FALSE
D71V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                       9
  17P LOSS WILD-TYPE                                     6
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                         1
  17P LOSS WILD-TYPE                                       0
                    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                                                           275
  17P LOSS WILD-TYPE                                                         195
D71V9, multiclass
                                                             clus
vv                                                            17P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              275
                                                             clus
vv                                                            17P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                195
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    10 278
  17P LOSS WILD-TYPE   3 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     10  278
  17P LOSS WILD-TYPE    3  202
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                10                  3
  YES              278                202
[1] 2 2
[1] FALSE
D71V11, continuous
D71V12, continuous
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   238   6   2  11
  17P LOSS WILD-TYPE 156   6   2  11
D71V13, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              238                156
  R1                6                  6
  R2                2                  2
  RX               11                 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
  17P LOSS MUTATED       6                        16   193
  17P LOSS WILD-TYPE     3                        15   147
D71V14, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    6                  3
  BLACK OR AFRICAN AMERICAN               16                 15
  WHITE                                  193                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"
D71V15, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4 173
  17P LOSS WILD-TYPE   4 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  173
  17P LOSS WILD-TYPE    4  136
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              173                136
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    60  32
  17Q LOSS WILD-TYPE 221 164
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                92                385 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                32                164 
$`17Q LOSS MUTATED`
TCGA-18-3410 TCGA-18-3414 TCGA-21-1070 TCGA-21-A5DI TCGA-22-1011 TCGA-22-1016 
        4.80        23.54       119.54        32.19         1.74        27.02 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4605 TCGA-22-5472 TCGA-22-5478 TCGA-22-5492 
       24.13         0.56        32.02        64.93         0.79        16.64 
TCGA-33-4583 TCGA-33-4587 TCGA-34-2600 TCGA-34-5241 TCGA-34-8455 TCGA-34-A5IX 
      151.27        54.44        61.61        16.93         4.04        20.91 
TCGA-37-4141 TCGA-39-5029 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 
        0.39        24.33        15.58        17.06        38.66        27.02 
TCGA-43-5670 TCGA-43-7656 TCGA-43-A56U TCGA-43-A56V TCGA-52-7622 TCGA-52-7810 
       27.91        19.59        14.20        12.03        28.34        30.35 
TCGA-56-5897 TCGA-56-5898 TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 
        0.10        18.25         1.32        17.49         1.35         1.18 
TCGA-56-8628 TCGA-56-A4ZJ TCGA-56-A62T TCGA-58-8393 TCGA-60-2695 TCGA-60-2696 
       20.25        21.04         2.76        34.78        21.11         3.58 
TCGA-60-2708 TCGA-60-2711 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 
       80.45        41.42        50.33        42.64         3.19        35.90 
TCGA-63-A5MG TCGA-63-A5MI TCGA-66-2769 TCGA-66-2771 TCGA-66-2780 TCGA-66-2782 
       70.62        58.65         7.07        19.00        12.03        12.00 
TCGA-66-2786 TCGA-77-7139 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 
       25.97        89.98        86.76        53.95        82.92        12.59 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8144 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5GB 
       53.92        17.72        27.39        54.41       132.36        30.81 
TCGA-77-A5GH TCGA-85-7696 TCGA-85-7697 TCGA-85-7950 TCGA-85-8479 TCGA-85-A4CN 
       38.86        36.53        34.95        18.94         0.72        19.33 
TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       17.72        18.18        16.21         0.79        12.39         3.65 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7557 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-A4JL 
        4.01         2.30         0.16        26.63        17.69        16.57 
TCGA-98-8021 TCGA-98-A538 TCGA-L3-A4E7 TCGA-NC-A5HF TCGA-NC-A5HQ TCGA-NK-A5CT 
       30.81        27.16        12.89         4.54        14.73        65.49 
TCGA-NK-A5CX TCGA-O2-A52Q 
        3.65         3.72 

$`17Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
       92.15        31.99        36.07         1.64        86.96         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 
        2.79       154.32        49.94        27.19        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-22-1000 TCGA-22-1002 
       33.93        10.82        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
       64.21        14.10        48.82        20.48        35.08        48.33 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       38.17        34.75        13.12        19.30         9.57        11.77 
TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
       31.73        63.55        14.63        44.25        54.28        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-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       22.06         7.63       133.74        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
      103.53        14.07         1.55        19.76        27.02         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-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
       27.16         2.63        31.50        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        67.79        56.38         9.07        23.24        12.00 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 
       30.94        18.15         4.96         1.12        27.19        26.43 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        3.95         0.43         0.39         6.58         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        7.82         6.81         3.39        47.80        74.07        44.75 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
       68.58        55.20        70.03        60.79         1.71         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 
       27.39        36.39        35.64        35.70        17.88        40.21 
TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       22.49        33.11        18.38        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        5.46         3.81         7.76        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
        2.93        11.61         9.73         9.99        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
        0.39         0.39        29.95         5.46         8.75        27.45 
TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
       28.96         2.04         0.62         0.99         0.43         0.99 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        1.45         0.85         6.51         0.10         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 
       17.00        14.07        16.77         1.81        22.75        10.36 
TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
        9.93        15.81        20.94        19.23        13.32        17.85 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.13         0.26         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       29.95        71.24        16.47        85.12        34.36        56.65 
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-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 
       92.71        21.93        49.48        66.54         9.01        56.91 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 
       35.34        48.49        32.32        29.85        23.57        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
       11.77       102.67        66.61        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       11.34        25.28        89.29        78.28        16.37        25.41 
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-66-2757 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-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        2.01         2.01        23.01         3.02         2.01        19.00 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
        3.98        24.95         1.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       49.05         2.73         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       16.18        14.73        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       11.18        20.78         0.49        42.28        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8128 TCGA-77-8136 
        0.16        46.78        15.75         6.51        37.81        39.09 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
      104.09        11.54        26.40         6.97         9.63        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       35.90         0.33       126.18       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       42.41        42.08        27.62         9.67        11.97        12.99 
TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
        6.41        31.30        32.91         1.38         1.15        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        14.07        16.87 
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-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
        5.29         3.09        32.71         2.01         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC 
       13.94        12.59         0.10        15.62        25.68        14.96 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-90-6837 
       24.36        19.73        12.56        15.85        14.96        24.92 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
        9.50         2.93        11.77        14.07        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 
       10.59         2.70         3.48         5.26        21.04        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 
        4.01         5.03        14.14        16.14        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 
       18.31        17.46        19.36         8.42         2.76        30.67 
TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       21.34         3.88        18.15         2.01        27.02        21.21 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
       20.32        18.58        20.71        19.10        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HH 
       13.41        11.84         0.07        64.08        51.78         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN 
       45.37        13.74         4.21         2.89        39.85        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5D1 
       30.58        24.00        29.75        22.78        83.57        16.80 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
        0.43        33.07        12.72        43.89         8.58        11.18 
TCGA-XC-AA0X 
        0.20 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            151.27             174.08 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             19.46              19.04 
[1] "0.1 - 151.3 (19.5)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.2"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0       20       29        0         9        18
  17Q LOSS WILD-TYPE       2       67      122        2        54        74
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  17Q LOSS MUTATED           1         13          2        2
  17Q LOSS WILD-TYPE         2         49         19        5
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 20                 67
  STAGE IB                 29                122
  STAGE II                  0                  2
  STAGE IIA                 9                 54
  STAGE IIB                18                 74
  STAGE III                 1                  2
  STAGE IIIA               13                 49
  STAGE IIIB                2                 19
  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  48  18   4
  17Q LOSS WILD-TYPE  87 242  51  19
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               24                 87
  T2               48                242
  T3               18                 51
  T4                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                  N0  N1  N2  N3
  17Q LOSS MUTATED    67  16   8   0
  17Q LOSS WILD-TYPE 245 115  31   5
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               67                245
  N1               16                115
  N2                8                 31
  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    78   2
  17Q LOSS WILD-TYPE 326   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     78    2
  17Q LOSS WILD-TYPE  326    5
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               78                326
  1                2                  5
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    31  63
  17Q LOSS WILD-TYPE  96 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     31   63
  17Q LOSS WILD-TYPE   96  303
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               31                 96
  MALE                 63                303
[1] 2 2
[1] FALSE
D72V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                       1
  17Q LOSS WILD-TYPE                                    14
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                         0
  17Q LOSS WILD-TYPE                                       1
                    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                                                            91
  17Q LOSS WILD-TYPE                                                         379
D72V9, multiclass
                                                             clus
vv                                                            17Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               91
                                                             clus
vv                                                            17Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                379
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     5  89
  17Q LOSS WILD-TYPE   8 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5   89
  17Q LOSS WILD-TYPE    8  391
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 5                  8
  YES               89                391
[1] 2 2
[1] FALSE
D72V11, continuous
D72V12, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    74   2   0   6
  17Q LOSS WILD-TYPE 320  10   4  16
D72V13, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               74                320
  R1                2                 10
  R2                0                  4
  RX                6                 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
  17Q LOSS MUTATED       4                         8    59
  17Q LOSS WILD-TYPE     5                        23   281
D72V14, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                8                 23
  WHITE                                   59                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"
D72V15, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2  63
  17Q LOSS WILD-TYPE   6 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   63
  17Q LOSS WILD-TYPE    6  246
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               63                246
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    87  52
  18P LOSS WILD-TYPE 194 144
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               139                338 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                52                144 
$`18P LOSS MUTATED`
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 TCGA-21-1071 
       23.54        92.15        36.07        86.96       119.54        46.88 
TCGA-21-1080 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1012 TCGA-22-1016 
      122.43        10.82        32.19        14.93        14.10        27.02 
TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4601 TCGA-22-5478 TCGA-22-5482 
       48.82        35.08        48.33        34.75         0.79        11.74 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4589 TCGA-33-6737 
      133.74        98.01        79.53       103.53         1.55        19.76 
TCGA-33-6738 TCGA-33-A5GW TCGA-34-2608 TCGA-34-2609 TCGA-34-5241 TCGA-34-7107 
       27.02         0.30        32.88        31.27        16.93         1.12 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        4.04        26.43        20.91         8.12         7.46         7.82 
TCGA-39-5011 TCGA-39-5028 TCGA-39-5036 TCGA-43-3394 TCGA-43-6647 TCGA-43-7656 
       47.80         1.71        35.64        27.02        24.89        19.59 
TCGA-43-8115 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-52-7810 TCGA-56-1622 
       13.38         9.99        10.65         0.39        30.35        28.96 
TCGA-56-5897 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-8307 TCGA-56-8503 
        0.10         2.04         0.99         0.43        26.89         1.35 
TCGA-56-8624 TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T 
        1.18         9.93        15.81        19.23        18.74         2.76 
TCGA-58-A46K TCGA-58-A46M TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2720 
       34.36        35.24        92.71        21.93        80.45         3.19 
TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
      102.67        66.61        25.28        89.29        78.28        16.37 
TCGA-63-A5MY TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2766 TCGA-66-2773 
       34.59         0.99         1.02         0.92         1.02         3.02 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2790 TCGA-66-2791 
       12.03         3.98         1.97        25.97        22.98         5.03 
TCGA-66-2792 TCGA-66-2795 TCGA-68-7757 TCGA-68-8250 TCGA-77-6842 TCGA-77-8007 
       30.02         4.01         6.94         8.02        29.56         6.51 
TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-A5G1 
       12.59        39.09       104.09        11.54        27.39       132.36 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 
        5.92        42.41        38.86         9.67        11.97        34.95 
TCGA-85-7950 TCGA-85-8287 TCGA-85-8355 TCGA-85-8481 TCGA-85-8584 TCGA-85-A4JC 
       18.94         0.76         2.01         7.76        12.59        14.96 
TCGA-85-A4QR TCGA-85-A511 TCGA-85-A53L TCGA-90-7766 TCGA-90-7767 TCGA-90-A4ED 
       19.73        14.96        12.39         9.50         2.93        20.22 
TCGA-92-7341 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I6 TCGA-96-8170 TCGA-96-A4JK 
        3.48         0.16        11.70        17.69        17.46        19.36 
TCGA-98-8020 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
        2.76        21.34        27.16         3.88        18.15         2.01 
TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HM 
       20.71        11.84         0.07        64.08        51.78        39.85 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52Q 
       30.58        24.00        29.75        65.49        16.80         3.72 
TCGA-O2-A52S 
       12.72 

$`18P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       11.34        31.99         1.64         6.18         2.79       154.32 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
       49.94        27.19        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-22-4613 TCGA-22-5471 
       13.12        32.02        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
       64.93        63.55        14.63        44.25        54.28        71.34 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       79.20        18.84        30.12        62.86        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       22.06         7.63       174.08       151.27        14.07        54.44 
TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        4.70        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-5231 
       27.16         2.63        61.61        31.50        28.96        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
       67.79        56.38         9.07        23.24        12.00        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       18.15         4.96        27.19         3.95         0.43         0.39 
TCGA-37-4129 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
        6.58         6.81         0.39         3.39        74.07        44.75 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 
       68.58        55.20        70.03        60.79        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
       27.39        36.39        15.58        35.70        17.88        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       40.21        22.49        38.66        33.11        18.38        27.91 
TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 
       12.36        21.47         5.46         3.81         7.76        66.51 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
       11.77         2.93        11.61         9.73        14.20        12.03 
TCGA-46-6026 TCGA-51-4080 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-52-7812 TCGA-56-5898 TCGA-56-6546 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       27.45        18.25         0.62         0.99         1.45         1.32 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 
        0.85         6.51         0.10        17.49         3.48        17.00 
TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 
       14.07        16.77         1.81        22.75        10.36        20.25 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
       20.94        13.32        17.85        21.04         0.13         0.26 
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-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
       34.78        85.12        56.65        29.92        21.11         3.58 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 
       12.23        10.22        96.82        37.94        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       41.42         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64        32.32        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
       11.77        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 
       11.34        25.41        36.16        53.88        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        2.01        21.07         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-66-2777 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 
       23.01        19.00         2.01        19.00        12.00        24.95 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
       40.01        22.98         4.04        10.06        54.08        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 
        2.73         6.64        13.35        16.18        14.73        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       75.09        23.28        11.18        89.98        20.78         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       42.28        70.13       106.95         0.16        46.78        15.75 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 
       86.76        53.95        37.81        82.92        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         9.63        54.41        65.49        35.90 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GA TCGA-77-A5GB 
        0.33       126.18       117.57        22.29        42.08        30.81 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
       27.62        12.99         6.41        36.53        31.30        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-85-8276 TCGA-85-8277 TCGA-85-8288 
       31.56        14.07        16.87        34.52        10.09        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 
       22.45        16.77         5.29         3.09        32.71         0.72 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       14.63        13.94         0.10        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       17.72        24.36        18.18        12.56        16.21        15.85 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
        0.79         3.65        24.92        11.77        14.07        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
       10.59         2.70         4.01         5.26         2.30        21.04 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 
        4.01         5.03        26.63        14.14        16.14        49.87 
TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       57.07        18.31        16.57         8.42        30.81        30.67 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 
       27.02        21.21        20.32        18.58        19.10        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        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HT 
       13.74         4.21         2.89        37.22        14.73        22.78 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A52W 
       83.57         3.65         0.43        33.07        43.89         8.58 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            133.74             174.08 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             18.15              19.79 
[1] "0.1 - 133.7 (18.1)" "0.0 - 174.1 (19.8)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         0       19       44        1        15        32
  18P LOSS WILD-TYPE       2       68      107        1        48        60
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  18P LOSS MUTATED           2         16          3        5
  18P LOSS WILD-TYPE         1         46         18        2
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 19                 68
  STAGE IB                 44                107
  STAGE II                  1                  1
  STAGE IIA                15                 48
  STAGE IIB                32                 60
  STAGE III                 2                  1
  STAGE IIIA               16                 46
  STAGE IIIB                3                 18
  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    24  86  22   7
  18P LOSS WILD-TYPE  87 204  47  16
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               24                 87
  T2               86                204
  T3               22                 47
  T4                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                  N0  N1  N2  N3
  18P LOSS MUTATED    90  36  10   1
  18P LOSS WILD-TYPE 222  95  29   4
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               90                222
  N1               36                 95
  N2               10                 29
  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   111   5
  18P LOSS WILD-TYPE 293   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    111    5
  18P LOSS WILD-TYPE  293    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              111                293
  1                5                  2
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    31 108
  18P LOSS WILD-TYPE  96 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     31  108
  18P LOSS WILD-TYPE   96  258
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               31                 96
  MALE                108                258
[1] 2 2
[1] FALSE
D73V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                       4
  18P LOSS WILD-TYPE                                    11
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                         0
  18P LOSS WILD-TYPE                                       1
                    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                                                           133
  18P LOSS WILD-TYPE                                                         337
D73V9, multiclass
                                                             clus
vv                                                            18P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              133
                                                             clus
vv                                                            18P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                337
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1 138
  18P LOSS WILD-TYPE  12 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1  138
  18P LOSS WILD-TYPE   12  342
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 1                 12
  YES              138                342
[1] 2 2
[1] FALSE
D73V11, continuous
D73V12, continuous
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED   108   3   0   5
  18P LOSS WILD-TYPE 286   9   4  17
D73V13, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              108                286
  R1                3                  9
  R2                0                  4
  RX                5                 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    90
  18P LOSS WILD-TYPE     7                        20   250
D73V14, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               11                 20
  WHITE                                   90                250
[1] 3 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  85
  18P LOSS WILD-TYPE   5 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   85
  18P LOSS WILD-TYPE    5  224
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               85                224
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   117  67
  18Q LOSS WILD-TYPE 164 129
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               184                293 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                67                129 
$`18Q LOSS MUTATED`
TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 
       11.34        23.54        31.99        36.07        86.96       119.54 
TCGA-21-1071 TCGA-21-1079 TCGA-21-1080 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 
       46.88        31.73       122.43        31.63        33.93        10.82 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4599 
       32.19        14.93        27.02        48.82        35.08        38.17 
TCGA-22-4601 TCGA-22-5473 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       34.75        63.55        22.06       133.74        98.01        79.53 
TCGA-33-4583 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AASD 
      151.27         1.55        19.76        27.02         0.30       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2608 TCGA-34-5231 TCGA-34-5241 TCGA-34-8454 
       44.19        27.16        32.88        65.23        16.93        27.19 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 
        4.04        20.91         0.43         0.39         8.12         7.82 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5027 TCGA-39-5028 TCGA-39-5036 TCGA-43-2576 
       47.80        74.07        60.79         1.71        35.64        40.21 
TCGA-43-3394 TCGA-43-5668 TCGA-43-6647 TCGA-43-7656 TCGA-46-3768 TCGA-46-6025 
       27.02        18.38        24.89        19.59         9.99        10.65 
TCGA-51-4079 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
        0.39        30.35        27.45        28.96         0.10         2.04 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        0.99         0.43         0.99         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY 
        1.35         1.18         9.93        15.81        19.23        17.85 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-A46K TCGA-58-A46M 
       18.74         0.13         2.76         0.03        34.36        35.24 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 
        3.58        10.22        92.71        21.93        80.45        50.33 
TCGA-60-2720 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5MP 
        3.19        11.77       102.67        66.61        59.97        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW TCGA-66-2734 
       89.29        78.28        16.37        25.41        53.88        43.10 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
        0.99         1.02         0.99         2.01         1.02         2.01 
TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2790 
        3.02        12.03         3.98         1.97        25.97        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59J 
        5.03        30.02         4.01         6.94         8.02        14.73 
TCGA-77-6842 TCGA-77-7337 TCGA-77-8007 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 
       29.56       106.95         6.51        82.92        12.59        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-A5G1 
       17.72       104.09        11.54        27.39         9.63       132.36 
TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 
       42.41        38.86         9.67        11.97        34.95        31.30 
TCGA-85-7844 TCGA-85-8049 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8352 
       29.95        19.04        16.87        34.52         0.76         5.29 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8584 TCGA-85-A4JC TCGA-85-A4QQ 
        3.09         2.01         7.76        12.59        14.96        18.18 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-90-7766 TCGA-90-7767 
       16.21        15.85        14.96        12.39         9.50         2.93 
TCGA-90-7769 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-94-7033 TCGA-94-7557 
       11.77        20.22         3.48         4.01        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       11.70        16.14        17.69        18.31        17.46        19.36 
TCGA-98-8020 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
        2.76        21.34        27.16         3.88        18.15         2.01 
TCGA-98-A53J TCGA-L3-A524 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
       20.71        16.11         0.07        64.08        51.78        45.37 
TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.21        39.85        37.22        30.58        24.00        14.73 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S 
       29.75        16.80         3.72        12.72 

$`18Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       92.15         1.64         6.18         2.79       154.32        49.94 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       27.19        99.16        70.16        60.89        34.78        15.58 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 
        9.34       119.80        43.23        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-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       48.33        24.13         0.56        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 
        9.57        11.77        31.73        64.93        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
        0.79        54.28        71.34        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4566 
       30.12        62.86        56.32        16.64         7.63       174.08 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB 
      103.53        14.07        54.44         4.70        36.62         6.94 
TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      118.36         2.63        61.61        31.50        28.96        31.27 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
       67.79        56.38         9.07        23.24        12.00        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-3783 TCGA-37-4129 
       18.15         4.96         1.12        26.43         3.95         6.58 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 
        7.46         6.81         0.39         3.39        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       55.20        70.03        24.33         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 
       15.58        35.70        17.88        17.06        22.49        38.66 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       33.11        27.91        12.36        21.47         5.46         3.81 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        7.76        66.51        13.38        11.77         2.93        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 
        9.73        14.20        12.03        13.91         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 TCGA-56-6546 TCGA-56-7579 
       28.34         5.46         8.75        18.25         0.62         1.45 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8308 
        1.32         0.85         6.51         0.10        17.49        17.00 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D 
       16.77         1.81        22.75        10.36        20.25        20.94 
TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       13.32        21.04         0.26        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N 
       71.24        16.47        34.78        85.12        56.65        29.92 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 
       21.11        12.23        96.82        37.94        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
       41.42         9.01        56.91        35.34        48.49        42.64 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG 
       32.32        29.85        35.90        23.57        26.83        70.62 
TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MV TCGA-63-A5MY 
       58.65        45.57        14.99        11.34        36.16        34.59 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       16.96         2.01        21.07         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 
       43.99        21.01        25.05         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 TCGA-66-2787 
       19.00         2.01        19.00        12.00        24.95        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 
       22.98         4.04        10.06        54.08        49.05         2.73 
TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
        6.64        13.35        16.18        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       11.18        89.98        20.78         0.49        42.28        70.13 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
        0.16        46.78        15.75        86.76        53.95        37.81 
TCGA-77-8133 TCGA-77-8143 TCGA-77-8145 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       53.92        26.40         6.97        54.41        65.49        35.90 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA 
        0.33       126.18       117.57        22.29         5.92        42.08 
TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 
       30.81        27.62        12.99         6.41        36.53        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 
        1.38         1.15        18.94        25.15        24.13        31.56 
TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 
       14.07        10.09        13.22        22.45        16.77        32.71 
TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
        0.72        14.63        13.94         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A513 
       19.33        17.72        24.36        19.73        12.56         0.79 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        3.65        24.92        14.07        22.62        10.59         2.70 
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-96-7545 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       49.87        57.07        16.57         8.42        30.81        30.67 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 
       27.02        21.21        20.32        18.58        19.10        12.89 
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-A5HL TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE 
        2.89        22.78        83.57        65.49         3.65         0.43 
TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07        43.89         8.58        11.18         0.20 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.03               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            151.27             174.08 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            18.345             19.730 
[1] "0.0 - 151.3 (18.3)" "0.1 - 174.1 (19.7)"
[1] "hr=" "1.2"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         0       25       57        0        25        44
  18Q LOSS WILD-TYPE       2       62       94        2        38        48
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  18Q LOSS MUTATED           2         24          3        5
  18Q LOSS WILD-TYPE         1         38         18        2
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                 25                 62
  STAGE IB                 57                 94
  STAGE II                  0                  2
  STAGE IIA                25                 38
  STAGE IIB                44                 48
  STAGE III                 2                  1
  STAGE IIIA               24                 38
  STAGE IIIB                3                 18
  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    33 114  33   7
  18Q LOSS WILD-TYPE  78 176  36  16
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               33                 78
  T2              114                176
  T3               33                 36
  T4                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                  N0  N1  N2  N3
  18Q LOSS MUTATED   114  56  13   1
  18Q LOSS WILD-TYPE 198  75  26   4
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              114                198
  N1               56                 75
  N2               13                 26
  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   146   5
  18Q LOSS WILD-TYPE 258   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    146    5
  18Q LOSS WILD-TYPE  258    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              146                258
  1                5                  2
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    44 143
  18Q LOSS WILD-TYPE  83 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     44  143
  18Q LOSS WILD-TYPE   83  223
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               44                 83
  MALE                143                223
[1] 2 2
[1] FALSE
D74V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                       5
  18Q LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                         0
  18Q LOSS WILD-TYPE                                       1
                    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                                                           179
  18Q LOSS WILD-TYPE                                                         291
D74V9, multiclass
                                                             clus
vv                                                            18Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              179
                                                             clus
vv                                                            18Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                291
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3 184
  18Q LOSS WILD-TYPE  10 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3  184
  18Q LOSS WILD-TYPE   10  296
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 3                 10
  YES              184                296
[1] 2 2
[1] FALSE
D74V11, continuous
D74V12, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   149   3   0  12
  18Q LOSS WILD-TYPE 245   9   4  10
D74V13, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              149                245
  R1                3                  9
  R2                0                  4
  RX               12                 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
  18Q LOSS MUTATED       3                        15   127
  18Q LOSS WILD-TYPE     6                        16   213
D74V14, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN               15                 16
  WHITE                                  127                213
[1] 3 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     4 119
  18Q LOSS WILD-TYPE   4 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4  119
  18Q LOSS WILD-TYPE    4  190
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              119                190
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    95  61
  19P LOSS WILD-TYPE 186 135
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               156                321 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                61                135 
$`19P LOSS MUTATED`
TCGA-18-3409 TCGA-18-3412 TCGA-18-3417 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       79.46        11.34        36.07        49.94       119.54        46.88 
TCGA-21-1077 TCGA-21-1081 TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-21-A5DI 
       34.78         9.34        43.23        88.11        33.93        32.19 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-4594 TCGA-22-4601 TCGA-22-4605 
       21.99         4.31        64.21        48.33        34.75        32.02 
TCGA-22-4607 TCGA-22-5478 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
       19.30         0.79        30.12        16.64        22.06         7.63 
TCGA-33-4582 TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASB TCGA-33-AASI 
      103.53        54.44        19.76        27.02         6.94        44.19 
TCGA-34-2604 TCGA-34-2608 TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 TCGA-34-8456 
       31.50        32.88        16.93        18.15         4.96        26.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.39         6.58         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5029 TCGA-39-5036 TCGA-43-2576 
        0.39         3.39        47.80        24.33        35.64        40.21 
TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6771 TCGA-43-7656 
       22.49        27.02        18.38        27.91         5.46        19.59 
TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 TCGA-52-7810 
       11.61        12.03        10.65        13.91        29.95        30.35 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 
        8.75        28.96         0.10        18.25         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-7822 TCGA-56-8624 TCGA-56-8629 
        0.99         1.45         6.51        17.49         1.18        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 
       20.94        13.32        21.04         0.13         2.76         0.03 
TCGA-58-8388 TCGA-58-8390 TCGA-58-A46L TCGA-60-2696 TCGA-60-2706 TCGA-60-2707 
       13.55        29.95        56.65         3.58        92.71        21.93 
TCGA-60-2711 TCGA-60-2714 TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MI TCGA-63-A5MP 
       41.42        50.33        29.85        35.90        58.65        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-66-2727 TCGA-66-2753 TCGA-66-2756 
       89.29        78.28        36.16        16.96         1.02         0.99 
TCGA-66-2759 TCGA-66-2769 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 
       25.05         7.07        12.03         3.98        12.00        25.97 
TCGA-66-2788 TCGA-66-2793 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-77-6845 
       22.98        10.06         2.73         6.64         8.02        23.28 
TCGA-77-7138 TCGA-77-7338 TCGA-77-7463 TCGA-77-8136 TCGA-77-8138 TCGA-77-8143 
       11.18         0.16        46.78        39.09        17.72        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8156 TCGA-85-6560 TCGA-85-7697 TCGA-85-8070 
       27.39         6.97         0.33        11.97        34.95        31.56 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8351 TCGA-85-8584 TCGA-85-A4CL 
       16.87        34.52         0.76        16.77        12.59        25.68 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A510 TCGA-85-A53L TCGA-90-7964 TCGA-90-A4ED 
       17.72        14.96        15.85        12.39        14.07        20.22 
TCGA-92-7341 TCGA-92-8063 TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I6 
        3.48         4.01         0.16        11.70        14.14        17.69 
TCGA-96-8169 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J TCGA-L3-A524 
       18.31         3.88        18.15         2.01        20.71        16.11 
TCGA-NC-A5HD TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN 
        0.07        51.78        45.37        13.74         4.21        37.22 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q 
       24.00        14.73        65.49        16.80        33.07         3.72 

$`19P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
       12.20         7.46        75.75         4.80       117.57        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       92.15        31.99         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 
      154.32        27.19        99.16        70.16        60.89        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 
       31.73       122.43       119.80        31.63        41.69        10.82 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
        7.33        14.93         1.74        14.10        27.02        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
       20.48        35.08        24.13         0.56        38.17        13.12 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
        9.57        11.77        31.73        64.93        63.55        14.63 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       44.25        54.28        71.34        79.20        11.74        18.84 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        56.32       133.74        98.01        79.53       174.08 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      151.27        14.07         1.55         4.70         0.30        36.62 
TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
      110.99       118.36        27.16         2.63        61.61        28.96 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.27        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5927 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX 
       12.00        30.94         1.12        27.19         4.04        20.91 
TCGA-37-3783 TCGA-37-3789 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        3.95         0.43        74.07        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       70.03        60.79         1.71         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2581 TCGA-43-3920 
       15.58        35.70        17.88        17.06        38.66        33.11 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 
       12.36        24.89        21.47         3.81         7.76        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 
       13.38        11.77         2.93         9.73        14.20         9.99 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-6545 
        0.39         0.39        28.34         5.46        27.45         2.04 
TCGA-56-6546 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        0.62         1.32         0.85         0.10         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
       17.00        14.07         1.35        16.77         1.81        22.75 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZK 
       10.36         9.93        20.25        19.23        17.85        18.74 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
        0.26        13.25        71.24        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 
       34.36        35.24        29.92        21.11        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
       96.82        37.94        80.45        49.48        66.54         9.01 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       56.91        35.34        48.49        42.64         3.19        32.32 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH 
       23.57        26.83        11.77       102.67        70.62        66.61 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MT TCGA-63-A5MU 
       59.97        45.57        14.99        11.34        16.37        25.41 
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-66-2795 TCGA-66-2800 
       22.98         5.03        30.02        54.08         4.01        49.05 
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-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       75.09        89.98        20.78         0.49        42.28        70.13 
TCGA-77-7337 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
      106.95        15.75         6.51        86.76        53.95        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8148 
       82.92        12.59        53.92       104.09        11.54         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       54.41        65.49        35.90       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
       38.86         9.67        12.99         6.41        36.53        31.30 
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-85-8052 TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 
       19.04        24.13        14.07        10.09        13.22        22.45 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
        5.29         3.09        32.71         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4PA 
       14.63        13.94         0.10        15.62        19.33        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 
       18.18        19.73        12.56        16.21        14.96         0.79 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
        3.65        24.92         9.50         2.93        11.77        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 
       10.59         2.70         5.26         2.30        21.04         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 
        5.03        26.63        16.14        49.87        57.07        17.46 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       19.36        16.57         8.42         2.76        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
       21.34        27.16        27.02        21.21        20.32        18.58 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HE 
       19.10        12.89        13.18        13.41        11.84        64.08 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HR 
        4.54         1.22         2.89        39.85        30.58        29.75 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52S TCGA-O2-A52V 
       22.78        83.57         3.65         0.43        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        8.58        11.18         0.20 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.03               0.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            119.54             174.08 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             17.72              20.32 
[1] "0.0 - 119.5 (17.7)" "0.1 - 174.1 (20.3)"
[1] "hr=" "1.2"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         1       25       48        0        25        27
  19P LOSS WILD-TYPE       1       62      103        2        38        65
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  19P LOSS MUTATED           1         21          6        4
  19P LOSS WILD-TYPE         2         41         15        3
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 25                 62
  STAGE IB                 48                103
  STAGE II                  0                  2
  STAGE IIA                25                 38
  STAGE IIB                27                 65
  STAGE III                 1                  2
  STAGE IIIA               21                 41
  STAGE IIIB                6                 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
  19P LOSS MUTATED    36  96  21   8
  19P LOSS WILD-TYPE  75 194  48  15
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               36                 75
  T2               96                194
  T3               21                 48
  T4                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                  N0  N1  N2  N3
  19P LOSS MUTATED   112  31  16   0
  19P LOSS WILD-TYPE 200 100  23   5
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0              112                200
  N1               31                100
  N2               16                 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"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   132   4
  19P LOSS WILD-TYPE 272   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    132    4
  19P LOSS WILD-TYPE  272    3
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              132                272
  1                4                  3
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    36 125
  19P LOSS WILD-TYPE  91 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     36  125
  19P LOSS WILD-TYPE   91  241
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               36                 91
  MALE                125                241
[1] 2 2
[1] FALSE
D75V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                       5
  19P LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                         1
  19P LOSS WILD-TYPE                                       0
                    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                                                           152
  19P LOSS WILD-TYPE                                                         318
D75V9, multiclass
                                                             clus
vv                                                            19P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              152
                                                             clus
vv                                                            19P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                318
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     6 155
  19P LOSS WILD-TYPE   7 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6  155
  19P LOSS WILD-TYPE    7  325
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 6                  7
  YES              155                325
[1] 2 2
[1] FALSE
D75V11, continuous
D75V12, continuous
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED   122   6   1   7
  19P LOSS WILD-TYPE 272   6   3  15
D75V13, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0              122                272
  R1                6                  6
  R2                1                  3
  RX                7                 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
  19P LOSS MUTATED       2                        11   113
  19P LOSS WILD-TYPE     7                        20   227
D75V14, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               11                 20
  WHITE                                  113                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"
D75V15, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3 104
  19P LOSS WILD-TYPE   5 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3  104
  19P LOSS WILD-TYPE    5  205
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO              104                205
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    67  35
  19Q LOSS WILD-TYPE 214 161
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               102                375 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                35                161 
$`19Q LOSS MUTATED`
TCGA-18-3409 TCGA-18-3412 TCGA-18-3416 TCGA-18-5592 TCGA-21-1077 TCGA-21-A5DI 
       79.46        11.34        31.99        49.94        34.78        32.19 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-4594 TCGA-22-4607 TCGA-22-4613 
       21.99         7.33        64.21        48.33        19.30        11.77 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4586 TCGA-33-4587 TCGA-33-AASB TCGA-34-5929 
       22.06         7.63        14.07        54.44         6.94         4.96 
TCGA-34-8456 TCGA-37-4129 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5036 
       26.43         6.58         7.82         6.81         0.39        35.64 
TCGA-43-3394 TCGA-43-6771 TCGA-43-7656 TCGA-43-A474 TCGA-46-6025 TCGA-46-6026 
       27.02         5.46        19.59        11.61        10.65        13.91 
TCGA-51-4081 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       29.95        30.35         8.75        28.96         0.10        18.25 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7822 TCGA-56-A4BX TCGA-56-A62T 
        0.99         0.43         1.45        17.49        13.32         2.76 
TCGA-58-8386 TCGA-58-A46L TCGA-60-2696 TCGA-60-2706 TCGA-60-2707 TCGA-60-2711 
        0.03        56.65         3.58        92.71        21.93        41.42 
TCGA-60-2714 TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MS TCGA-66-2727 TCGA-66-2753 
       50.33        58.65        25.28        78.28        16.96         1.02 
TCGA-66-2756 TCGA-66-2759 TCGA-66-2781 TCGA-66-2782 TCGA-66-2794 TCGA-68-7755 
        0.99        25.05         3.98        12.00        54.08         2.73 
TCGA-68-7756 TCGA-68-8250 TCGA-77-6845 TCGA-77-7338 TCGA-77-7463 TCGA-77-8136 
        6.64         8.02        23.28         0.16        46.78        39.09 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8156 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 
       26.40        27.39         0.33        11.97        12.99        34.95 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
        1.15        18.94        31.56        14.07        16.87        34.52 
TCGA-85-8287 TCGA-85-8351 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JC TCGA-90-A4ED 
        0.76        16.77        12.59        25.68        14.96        20.22 
TCGA-92-8063 TCGA-94-7943 TCGA-94-A4VJ TCGA-98-A539 TCGA-98-A53A TCGA-98-A53J 
        4.01        11.70        14.14         3.88        18.15        20.71 
TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ 
       16.11        11.84         0.07        51.78        45.37        13.74 
TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q 
        4.21        37.22        24.00        16.80        33.07         3.72 

$`19Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
       12.20         7.46        75.75         4.80       117.57        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       92.15        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      154.32        27.19       119.54        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       60.89        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-22-1000 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
       14.93         4.31         1.74        14.10        27.02        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       20.48        35.08        24.13         0.56        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       13.12        32.02         9.57        31.73        64.93        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        54.28        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-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
      133.74        98.01        79.53       174.08       103.53       151.27 
TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
        1.55        19.76        27.02         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-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
       31.50        28.96        32.88        31.27        65.23        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       56.38         9.07        23.24        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 
       18.15         1.12        27.19         4.04        20.91         3.95 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 
        0.43         0.39         8.12         7.46         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       74.07        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1.71        24.33         1.94        27.39        36.39        15.58 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       35.70        17.88        17.06        40.21        22.49        38.66 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       33.11        18.38        27.91        12.36        24.89        21.47 
TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        3.81         7.76        66.51        13.38        11.77         2.93 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-51-4079 TCGA-51-4080 
        9.73        14.20        12.03         9.99         0.39         0.39 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 
       28.34         5.46        27.45         2.04         0.62         0.99 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        1.32         0.85         6.51         0.10         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
       17.00        14.07         1.35        16.77         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.18        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
       19.23        17.85        21.04        18.74         0.13         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-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-60-2708 TCGA-60-2709 TCGA-60-2710 
       10.22        96.82        37.94        80.45        49.48        66.54 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
        9.01        56.91        35.34        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       32.32        29.85        35.90        23.57        26.83        11.77 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        66.61        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       11.34        89.29        16.37        25.41        36.16        53.88 
TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
       34.59        43.10         2.01        21.07         0.99         2.01 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
        0.92        43.99        21.01         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-66-2783 TCGA-66-2785 TCGA-66-2786 
        2.01        19.00        12.03        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-66-2795 TCGA-66-2800 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
       10.06         4.01        49.05         6.94        13.35        16.18 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 
       14.73        29.56        73.12        75.09        11.18        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 
       20.78         0.49        42.28        70.13       106.95        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        6.51        86.76        53.95        37.81        82.92        12.59 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 
       53.92        17.72       104.09        11.54         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       54.41        65.49        35.90       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
       38.86         9.67         6.41        36.53        31.30        32.91 
TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8277 
        1.38        29.95        25.15        19.04        24.13        10.09 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       13.22        22.45         5.29         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
        0.72         7.76        14.63        13.94         0.10        15.62 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       19.33        17.72        24.36        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96         0.79        12.39         3.65 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
       24.92         9.50         2.93        11.77        14.07        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
       10.59         2.70         3.48         5.26         2.30        21.04 
TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 
        0.16         4.01         5.03        26.63        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       49.87        57.07        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
        8.42         2.76        30.81        30.67        21.34        27.16 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH 
        2.01        27.02        21.21        20.32        18.58        19.10 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH 
       12.89        13.18        13.41        64.08         4.54         1.22 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT 
        2.89        39.85        30.58        14.73        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52S TCGA-O2-A52V 
       83.57        65.49         3.65         0.43        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        8.58        11.18         0.20 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.03               0.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             92.71             174.08 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            16.785             20.320 
[1] "0.0 - 92.7 (16.8)"  "0.1 - 174.1 (20.3)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         1       15       31        0        20        20
  19Q LOSS WILD-TYPE       1       72      120        2        43        72
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  19Q LOSS MUTATED           1         10          4        2
  19Q LOSS WILD-TYPE         2         52         17        5
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 15                 72
  STAGE IB                 31                120
  STAGE II                  0                  2
  STAGE IIA                20                 43
  STAGE IIB                20                 72
  STAGE III                 1                  2
  STAGE IIIA               10                 52
  STAGE IIIB                4                 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
  19Q LOSS MUTATED    23  64  15   5
  19Q LOSS WILD-TYPE  88 226  54  18
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               23                 88
  T2               64                226
  T3               15                 54
  T4                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                  N0  N1  N2  N3
  19Q LOSS MUTATED    70  25   9   0
  19Q LOSS WILD-TYPE 242 106  30   5
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               70                242
  N1               25                106
  N2                9                 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    88   2
  19Q LOSS WILD-TYPE 316   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     88    2
  19Q LOSS WILD-TYPE  316    5
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               88                316
  1                2                  5
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    19  88
  19Q LOSS WILD-TYPE 108 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     19   88
  19Q LOSS WILD-TYPE  108  278
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               19                108
  MALE                 88                278
[1] 2 2
[1] FALSE
D76V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED                                       4
  19Q LOSS WILD-TYPE                                    11
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED                                         0
  19Q LOSS WILD-TYPE                                       1
                    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                                                           100
  19Q LOSS WILD-TYPE                                                         370
D76V9, multiclass
                                                             clus
vv                                                            19Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              100
                                                             clus
vv                                                            19Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                370
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5 102
  19Q LOSS WILD-TYPE   8 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5  102
  19Q LOSS WILD-TYPE    8  378
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 5                  8
  YES              102                378
[1] 2 2
[1] FALSE
D76V11, continuous
D76V12, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    80   3   1   6
  19Q LOSS WILD-TYPE 314   9   3  16
D76V13, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               80                314
  R1                3                  9
  R2                1                  3
  RX                6                 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
  19Q LOSS MUTATED       1                         7    77
  19Q LOSS WILD-TYPE     8                        24   263
D76V14, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                7                 24
  WHITE                                   77                263
[1] 3 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  68
  19Q LOSS WILD-TYPE   6 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   68
  19Q LOSS WILD-TYPE    6  241
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               68                241
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    27  15
  20P LOSS WILD-TYPE 254 181
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                435 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                181 
$`20P LOSS MUTATED`
TCGA-18-3416 TCGA-18-4721 TCGA-21-1078 TCGA-21-5787 TCGA-22-4593 TCGA-22-5478 
       31.99       154.32        15.58        10.82        35.08         0.79 
TCGA-33-4583 TCGA-33-4586 TCGA-33-AASB TCGA-37-3792 TCGA-37-4135 TCGA-39-5034 
      151.27        14.07         6.94         0.39         6.81        36.39 
TCGA-43-3394 TCGA-43-6771 TCGA-52-7810 TCGA-56-8307 TCGA-60-2706 TCGA-60-2712 
       27.02         5.46        30.35        26.89        92.71         9.01 
TCGA-60-2714 TCGA-63-A5MH TCGA-66-2755 TCGA-66-2766 TCGA-66-2768 TCGA-66-2790 
       50.33        66.61         0.92         1.02         2.01        22.98 
TCGA-66-2791 TCGA-68-A59J TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8144 
        5.03        14.73       106.95        46.78        15.75        27.39 
TCGA-85-6560 TCGA-85-7950 TCGA-85-8071 TCGA-85-8352 TCGA-85-A4QR TCGA-85-A50Z 
       11.97        18.94        14.07         5.29        19.73        16.21 
TCGA-92-8065 TCGA-96-7544 TCGA-96-8169 TCGA-98-A538 TCGA-NC-A5HG TCGA-NC-A5HM 
        2.30        49.87        18.31        27.16        51.78        39.85 

$`20P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       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         1.64        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
        6.18         2.79        49.94        27.19       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-21-5783 TCGA-21-5784 
        9.34       119.80        43.23        31.63        88.11        41.69 
TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       33.93        32.19        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
       64.21         1.74        14.10        27.02        48.82        20.48 
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-22-5471 TCGA-22-5472 
       32.02        19.30         9.57        11.77        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       63.55        14.63        44.25        54.28        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-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       22.06         7.63       133.74        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
      103.53        54.44         1.55        19.76        27.02         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-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
        2.63        61.61        31.50        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        67.79        56.38         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        30.94        18.15         4.96         1.12        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
        4.04        26.43        20.91         3.95         0.43         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        8.12         7.46         7.82         0.39         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       74.07        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1.71        24.33         1.94        27.39        15.58        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       35.70        17.88        17.06        40.21        22.49        38.66 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       33.11        18.38        27.91        12.36        24.89        21.47 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        3.81        19.59         7.76        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
        2.93        11.61         9.73        14.20        12.03         9.99 
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-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        5.46         8.75        27.45        28.96         0.10        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
        2.04         0.62         0.99         0.43         0.99         1.45 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        1.32         0.85         6.51         0.10        17.49         3.48 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
       17.00        14.07         1.35        16.77         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.18        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       19.23        13.32        17.85        21.04        18.74         0.13 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26         2.76         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-60-2696 TCGA-60-2697 TCGA-60-2698 
       35.24        29.92        21.11         3.58        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-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       41.42        56.91        35.34        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       32.32        29.85        35.90        23.57        26.83        11.77 
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-A5MU 
       11.34        25.28        89.29        78.28        16.37        25.41 
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-66-2756 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-66-2767 TCGA-66-2769 
       21.01        25.05         0.99         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-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         4.04        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       49.05         2.73         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       16.18        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 
       89.98        20.78         0.49        42.28        70.13         0.16 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        6.51        86.76        53.95        37.81        82.92        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-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97         9.63        54.41        65.49        35.90         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       117.57        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 
       42.08        30.81        27.62        38.86         9.67        12.99 
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-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
        1.15        29.95        25.15        19.04        24.13        31.56 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       16.87        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         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       19.33        17.72        14.96        24.36        18.18        12.56 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       15.85        14.96         0.79        12.39         3.65        24.92 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
        9.50         2.93        11.77        14.07        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 
       10.59         2.70         3.48         4.01         5.26        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        0.16        11.70         4.01         5.03        26.63        14.14 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       16.14        17.69        57.07        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 
        8.42         2.76        30.81        30.67        21.34         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
       18.15         2.01        27.02        21.21        20.32        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       20.71        19.10        12.89        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI 
       11.84         0.07        64.08         4.54         1.22        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21         2.89        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       14.73        29.75        22.78        83.57        65.49         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       16.80         0.43        33.07         3.72        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        8.58        11.18         0.20 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.39               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            154.32             174.08 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            18.625             19.230 
[1] "0.4 - 154.3 (18.6)" "0.0 - 174.1 (19.2)"
[1] "hr=" "1.3"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         0        6       13        0         4        12
  20P LOSS WILD-TYPE       2       81      138        2        59        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  20P LOSS MUTATED           0          5          2        0
  20P LOSS WILD-TYPE         3         57         19        7
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  6                 81
  STAGE IB                 13                138
  STAGE II                  0                  2
  STAGE IIA                 4                 59
  STAGE IIB                12                 80
  STAGE III                 0                  3
  STAGE IIIA                5                 57
  STAGE IIIB                2                 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
  20P LOSS MUTATED     7  29   6   0
  20P LOSS WILD-TYPE 104 261  63  23
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                7                104
  T2               29                261
  T3                6                 63
  T4                0                 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
  20P LOSS MUTATED    26  11   4   1
  20P LOSS WILD-TYPE 286 120  35   4
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               26                286
  N1               11                120
  N2                4                 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"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    37   0
  20P LOSS WILD-TYPE 367   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     37    0
  20P LOSS WILD-TYPE  367    7
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               37                367
  1                0                  7
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8  34
  20P LOSS WILD-TYPE 119 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   34
  20P LOSS WILD-TYPE  119  332
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                119
  MALE                 34                332
[1] 2 2
[1] FALSE
D77V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED                                       1
  20P LOSS WILD-TYPE                                    14
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED                                         0
  20P LOSS WILD-TYPE                                       1
                    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                                                         429
D77V9, multiclass
                                                             clus
vv                                                            20P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG CLEAR CELL 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)               41
                                                             clus
vv                                                            20P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                429
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  41
  20P LOSS WILD-TYPE  12 439
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   41
  20P LOSS WILD-TYPE   12  439
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 1                 12
  YES               41                439
[1] 2 2
[1] FALSE
D77V11, continuous
D77V12, continuous
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    33   1   0   3
  20P LOSS WILD-TYPE 361  11   4  19
D77V13, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               33                361
  R1                1                 11
  R2                0                  4
  RX                3                 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
  20P LOSS MUTATED       0                         3    30
  20P LOSS WILD-TYPE     9                        28   310
D77V14, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                   30                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"
D77V15, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  26
  20P LOSS WILD-TYPE   8 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   26
  20P LOSS WILD-TYPE    8  283
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               26                283
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    25  20
  20Q LOSS WILD-TYPE 256 176
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                45                432 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                20                176 
$`20Q LOSS MUTATED`
TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 TCGA-18-4721 TCGA-21-1078 TCGA-22-4604 
      117.57        92.15        31.99       154.32        15.58        13.12 
TCGA-22-5478 TCGA-33-4583 TCGA-33-4586 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2600 
        0.79       151.27        14.07         6.94       118.36        61.61 
TCGA-34-7107 TCGA-39-5021 TCGA-39-5034 TCGA-43-3394 TCGA-46-6025 TCGA-52-7622 
        1.12        68.58        36.39        27.02        10.65        28.34 
TCGA-56-7580 TCGA-56-8307 TCGA-56-8308 TCGA-56-A49D TCGA-58-8392 TCGA-60-2698 
        1.32        26.89        17.00        20.94        16.47        10.22 
TCGA-60-2712 TCGA-60-2723 TCGA-63-A5MH TCGA-66-2755 TCGA-66-2766 TCGA-66-2791 
        9.01        35.90        66.61         0.92         1.02         5.03 
TCGA-68-A59J TCGA-77-7142 TCGA-77-8144 TCGA-77-8153 TCGA-77-8156 TCGA-85-7698 
       14.73        42.28        27.39        65.49         0.33        31.30 
TCGA-85-7950 TCGA-85-8071 TCGA-85-8352 TCGA-85-A4CN TCGA-92-8065 TCGA-96-A4JK 
       18.94        14.07         5.29        19.33         2.30        19.36 
TCGA-L3-A524 TCGA-NC-A5HL TCGA-NC-A5HN 
       16.11         2.89        37.22 

$`20Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 
       12.20         7.46        75.75        79.46         4.80        11.34 
TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       23.54        36.07         1.64        86.96         6.18         2.79 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
       49.94        27.19       119.54        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       60.89        34.78        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-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       32.19        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
        1.74        14.10        27.02        48.82        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-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
       14.63        44.25        54.28        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       18.84        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
        7.63       133.74        98.01        79.53       174.08       103.53 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       54.44         1.55        19.76        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2604 
       36.62       110.99        44.19        27.16         2.63        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       28.96        32.88        31.27        65.23        67.79        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        23.24        12.00        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        4.96        27.19         4.04        26.43        20.91         3.95 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         6.58         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        6.81         0.39         3.39        47.80        74.07        44.75 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        70.03        60.79         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
       27.39        15.58        35.64        35.70        17.88        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       40.21        22.49        38.66        33.11        18.38        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       12.36        24.89        21.47         5.46         3.81        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        7.76        66.51        13.38        11.77         2.93        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 
        9.73        14.20        12.03         9.99        13.91         0.39 
TCGA-51-4080 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-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
       28.96         0.10        18.25         2.04         0.62         0.99 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.43         0.99         1.45         0.85         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
       17.49         3.48        14.07         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       19.23        13.32        17.85        21.04        18.74         0.13 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26         2.76         0.03        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       71.24        34.78        85.12        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       29.92        21.11         3.58        12.23        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       92.71        21.93        80.45        49.48        66.54        41.42 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       56.91        50.33        35.34        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       32.32        29.85        23.57        26.83        11.77       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-A5MU TCGA-63-A5MV 
       25.28        89.29        78.28        16.37        25.41        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-68-8250 
        4.01        49.05         2.73         6.64         6.94         8.02 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       13.35        16.18        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       11.18        89.98        20.78         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        15.75         6.51        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       37.81        82.92        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         9.63        54.41 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       35.90       126.18       132.36       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       42.41        42.08        30.81        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
       11.97        12.99         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-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       31.56        16.87        34.52        10.09         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       22.45        16.77         3.09        32.71         2.01         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        7.76        14.63        13.94        12.59         0.10        15.62 
TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       25.68        17.72        14.96        24.36        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       12.56        16.21        15.85        14.96         0.79        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
        3.65        24.92         9.50         2.93        11.77        14.07 
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-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        5.26        21.04         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       26.63        14.14        16.14        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 
       18.31        17.46        16.57         8.42         2.76        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
       30.67        21.34        27.16         3.88        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
       27.02        21.21        20.32        18.58        20.71        19.10 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       12.89        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        51.78         1.22        45.37        13.74         4.21 
TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT 
       39.85        30.58        24.00        14.73        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N 
       83.57        65.49         3.65        16.80         0.43        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        12.72        43.89         8.58        11.18         0.20 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.33               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            154.32             174.08 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            18.940             19.165 
[1] "0.3 - 154.3 (18.9)" "0.0 - 174.1 (19.2)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         0        7       18        1         4        10
  20Q LOSS WILD-TYPE       2       80      133        1        59        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  20Q LOSS MUTATED           0          5          1        0
  20Q LOSS WILD-TYPE         3         57         20        7
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  7                 80
  STAGE IB                 18                133
  STAGE II                  1                  1
  STAGE IIA                 4                 59
  STAGE IIB                10                 82
  STAGE III                 0                  3
  STAGE IIIA                5                 57
  STAGE IIIB                1                 20
  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  33   6   0
  20Q LOSS WILD-TYPE 104 257  63  23
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                7                104
  T2               33                257
  T3                6                 63
  T4                0                 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
  20Q LOSS MUTATED    31  10   4   1
  20Q LOSS WILD-TYPE 281 121  35   4
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0               31                281
  N1               10                121
  N2                4                 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"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    40   0
  20Q LOSS WILD-TYPE 364   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     40    0
  20Q LOSS WILD-TYPE  364    7
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0               40                364
  1                0                  7
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    13  33
  20Q LOSS WILD-TYPE 114 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     13   33
  20Q LOSS WILD-TYPE  114  333
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               13                114
  MALE                 33                333
[1] 2 2
[1] FALSE
D78V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                    15
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED                                         0
  20Q LOSS WILD-TYPE                                       1
                    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                                                            46
  20Q LOSS WILD-TYPE                                                         424
D78V9, multiclass
                                                             clus
vv                                                            20Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      0
  LUNG CLEAR CELL 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)               46
                                                             clus
vv                                                            20Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       15
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                424
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  46
  20Q LOSS WILD-TYPE  13 434
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   46
  20Q LOSS WILD-TYPE   13  434
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 0                 13
  YES               46                434
[1] 2 2
[1] FALSE
D78V11, continuous
D78V12, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED    39   2   0   3
  20Q LOSS WILD-TYPE 355  10   4  19
D78V13, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               39                355
  R1                2                 10
  R2                0                  4
  RX                3                 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    31
  20Q LOSS WILD-TYPE     9                        28   309
D78V14, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                3                 28
  WHITE                                   31                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"
D78V15, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1  27
  20Q LOSS WILD-TYPE   7 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   27
  20Q LOSS WILD-TYPE    7  282
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               27                282
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   151  99
  21Q LOSS WILD-TYPE 130  97
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               250                227 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                99                 97 
$`21Q LOSS MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
       75.75       117.57        11.34        23.54        92.15        31.99 
TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 
       36.07         6.18         2.79       154.32       119.54        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
       70.16        60.89        31.73        43.23        33.93        10.82 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        7.33         4.31        14.10        27.02        48.82        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 
       35.08        48.33        38.17        13.12        11.77        31.73 
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        54.28        71.34 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 
       11.74        18.84        56.32         7.63        98.01        79.53 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI 
      103.53        14.07         1.55        36.62         6.94        44.19 
TCGA-33-AASL TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 TCGA-34-5236 TCGA-34-5241 
       27.16        31.50        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 
       30.94         1.12         4.04        26.43         0.43         0.39 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
        8.12         7.82         6.81         3.39        74.07        44.75 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 
       60.79        24.33        27.39        36.39        35.64        35.70 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 TCGA-43-6771 
       17.88        40.21        22.49        33.11        18.38         5.46 
TCGA-43-7656 TCGA-43-8116 TCGA-43-8118 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
       19.59        11.77         2.93        12.03         9.99        10.65 
TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
       13.91         0.39        29.95        28.34         5.46        30.35 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 
       28.96         0.10        18.25         2.04         0.62         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 
        0.99         1.45         1.32         0.85         6.51        17.49 
TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ 
        1.35        15.81        20.94        19.23        13.32        21.04 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 
        2.76         0.03        13.25        13.55        29.95        16.47 
TCGA-58-A46K TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 
       34.36        10.22        96.82        21.93        80.45        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        9.01        35.34        42.64        32.32        29.85        35.90 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN 
       26.83        11.77       102.67        59.97        45.57        11.34 
TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 
       25.28        78.28        36.16        53.88        34.59        43.10 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
       21.07         1.02         2.01         0.92        43.99        21.01 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 
       25.05         2.01         1.02        19.00         2.01        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        3.98        12.00         1.97        25.97        40.01        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
        5.03        30.02        10.06         4.01        49.05         2.73 
TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-7141 TCGA-77-7335 
        6.64         8.02        13.35        29.56         0.49        70.13 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8136 TCGA-77-8145 
       46.78        15.75        86.76        53.95        39.09         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 
        9.63        54.41        65.49        35.90         0.33       117.57 
TCGA-77-A5G6 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       22.29        27.62        38.86        12.99         6.41        36.53 
TCGA-85-7698 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 
       31.30         1.15        25.15        19.04        31.56        14.07 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
       34.52         0.76        22.45        16.77         5.29        32.71 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
        2.01         7.76         0.10        15.62        25.68        19.33 
TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L 
       14.96        19.73        16.21        15.85        14.96        12.39 
TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 
        3.65         9.50        11.77        20.22        22.62         3.48 
TCGA-92-8064 TCGA-94-7557 TCGA-94-7943 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
        5.26         0.16        11.70        26.63        14.14        16.14 
TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       17.69        19.36        30.81        30.67        21.34        27.16 
TCGA-98-A539 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 
        3.88        18.58        20.71        12.89        13.18        11.84 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM 
        0.07        64.08         1.22        13.74         4.21        39.85 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       24.00        14.73        83.57        65.49         3.65        16.80 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
        3.72        12.72        43.89         8.58 

$`21Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3419 TCGA-18-3421 
       12.20         7.46        79.46         4.80         1.64        86.96 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 
       49.94        27.19        46.88        34.78        15.58       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI 
        9.34       119.80        31.63        88.11        41.69        32.19 
TCGA-22-0940 TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-4595 TCGA-22-4596 
       21.99        14.93        64.21         1.74        24.13         0.56 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5472 TCGA-22-5481 
       34.75        32.02        19.30         9.57        64.93        79.20 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4566 
       30.12        62.86        16.64        22.06       133.74       174.08 
TCGA-33-4583 TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
      151.27        54.44        19.76        27.02         4.70         0.30 
TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 
      110.99       118.36         2.63        61.61        28.96        31.27 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-5929 
       67.79        56.38        23.24        12.00        18.15         4.96 
TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 TCGA-37-4129 TCGA-37-4132 TCGA-37-4141 
       27.19        20.91         3.95         6.58         7.46         0.39 
TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 
       47.80        68.58        55.20        70.03         1.71         1.94 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 
       15.58        17.06        38.66        27.02        27.91        12.36 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       24.89        21.47         3.81         7.76        66.51        13.38 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 TCGA-52-7811 TCGA-52-7812 
       11.61         9.73        14.20         0.39         8.75        27.45 
TCGA-56-7221 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.99         0.10         3.48        26.89        17.00        14.07 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       16.77         1.81        22.75         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8391 
       20.25        17.85        18.74         0.13         0.26        71.24 
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-60-2696 TCGA-60-2697 TCGA-60-2704 TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 
        3.58        12.23        37.94        92.71        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2724 TCGA-63-A5MG 
       56.91        50.33        48.49         3.19        23.57        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MU 
       66.61        58.65        14.99        89.29        16.37        25.41 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 TCGA-66-2767 
       16.96         2.01         0.99         0.99         0.99         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2778 TCGA-66-2783 
        2.01         7.07        23.01         3.02        19.00        24.95 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J 
        4.04        22.98        54.08         6.94        16.18        14.73 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 
       73.12        75.09        23.28        11.18        89.98        20.78 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 
       42.28       106.95         0.16         6.51        37.81        82.92 
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-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
       27.39       126.18       132.36         5.92        42.41        42.08 
TCGA-77-A5GB TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
       30.81         9.67        11.97        34.95        32.91         1.38 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 
       29.95        18.94        24.13        16.87        10.09        13.22 
TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB 
        3.09         0.72        14.63        13.94        12.59        17.72 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7767 
       24.36        18.18        12.56         0.79        24.92         2.93 
TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
       14.07        10.59         2.70         4.01         2.30        21.04 
TCGA-94-8035 TCGA-94-8490 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
        4.01         5.03        49.87        57.07        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       16.57         8.42         2.76        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HF 
       21.21        20.32        19.10        16.11        13.41         4.54 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HR 
       51.78        45.37         2.89        37.22        30.58        29.75 
TCGA-NC-A5HT TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A5IB TCGA-XC-AA0X 
       22.78         0.43        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             174.08 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             19.02              19.30 
[1] "0.0 - 154.3 (19.0)" "0.1 - 174.1 (19.3)"
[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       80        2        37        43
  21Q LOSS WILD-TYPE       1       38       71        0        26        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  21Q LOSS MUTATED           2         29          9        6
  21Q LOSS WILD-TYPE         1         33         12        1
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 49                 38
  STAGE IB                 80                 71
  STAGE II                  2                  0
  STAGE IIA                37                 26
  STAGE IIB                43                 49
  STAGE III                 2                  1
  STAGE IIIA               29                 33
  STAGE IIIB                9                 12
  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    58 157  32  12
  21Q LOSS WILD-TYPE  53 133  37  11
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               58                 53
  T2              157                133
  T3               32                 37
  T4               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                  N0  N1  N2  N3
  21Q LOSS MUTATED   167  69  19   1
  21Q LOSS WILD-TYPE 145  62  20   4
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0              167                145
  N1               69                 62
  N2               19                 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   219   6
  21Q LOSS WILD-TYPE 185   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    219    6
  21Q LOSS WILD-TYPE  185    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              219                185
  1                6                  1
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    49 210
  21Q LOSS WILD-TYPE  78 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     49  210
  21Q LOSS WILD-TYPE   78  156
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               49                 78
  MALE                210                156
[1] 2 2
[1] FALSE
D79V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                       7
  21Q LOSS WILD-TYPE                                     8
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                         1
  21Q LOSS WILD-TYPE                                       0
                    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                                                           249
  21Q LOSS WILD-TYPE                                                         221
D79V9, multiclass
                                                             clus
vv                                                            21Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG CLEAR CELL 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)              249
                                                             clus
vv                                                            21Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                221
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     7 252
  21Q LOSS WILD-TYPE   6 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7  252
  21Q LOSS WILD-TYPE    6  228
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 7                  6
  YES              252                228
[1] 2 2
[1] FALSE
D79V11, continuous
D79V12, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   207   6   2  10
  21Q LOSS WILD-TYPE 187   6   2  12
D79V13, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              207                187
  R1                6                  6
  R2                2                  2
  RX               10                 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
  21Q LOSS MUTATED       3                        14   178
  21Q LOSS WILD-TYPE     6                        17   162
D79V14, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN               14                 17
  WHITE                                  178                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V15, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     6 157
  21Q LOSS WILD-TYPE   2 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6  157
  21Q LOSS WILD-TYPE    2  152
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO              157                152
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    52  42
  22Q LOSS WILD-TYPE 229 154
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                94                383 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                42                154 
$`22Q LOSS MUTATED`
TCGA-18-3407 TCGA-18-3417 TCGA-18-4083 TCGA-21-1070 TCGA-21-1071 TCGA-21-1080 
        7.46        36.07         6.18       119.54        46.88       122.43 
TCGA-21-5783 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1016 TCGA-22-4594 
       88.11        10.82        32.19        21.99        27.02        48.33 
TCGA-22-5480 TCGA-22-5483 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6737 
       71.34        18.84       103.53       151.27        54.44        19.76 
TCGA-33-AAS8 TCGA-33-AASB TCGA-34-5928 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
       36.62         6.94        18.15         0.39         6.58         7.46 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5029 TCGA-39-5040 TCGA-43-2578 
        3.39        47.80        74.07        24.33        17.06        22.49 
TCGA-43-2581 TCGA-43-6771 TCGA-43-7658 TCGA-52-7812 TCGA-56-6546 TCGA-56-7222 
       38.66         5.46        66.51        27.45         0.62         0.43 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-A62T TCGA-60-2695 TCGA-63-A5MJ 
        3.48        26.89        14.07         2.76        21.11        59.97 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 
       11.34        25.28        34.59        16.96         1.02         2.01 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2766 TCGA-66-2771 TCGA-66-2778 TCGA-66-2782 
       43.99        25.05         1.02        19.00        19.00        12.00 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-68-8250 TCGA-68-A59I 
        4.04        22.98         5.03        10.06         8.02        16.18 
TCGA-77-7138 TCGA-77-7337 TCGA-77-7465 TCGA-77-8139 TCGA-77-8150 TCGA-77-A5G6 
       11.18       106.95        15.75       104.09        54.41        22.29 
TCGA-85-6560 TCGA-85-7697 TCGA-85-8048 TCGA-85-8049 TCGA-85-8072 TCGA-85-8584 
       11.97        34.95        25.15        19.04        16.87        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A510 TCGA-85-A53L TCGA-90-A4ED TCGA-90-A4EE 
        0.10        15.62        15.85        12.39        20.22        22.62 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-98-7454 TCGA-98-A53B TCGA-MF-A522 
       10.59         4.01         2.30         8.42         2.01        11.84 
TCGA-NC-A5HE TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ 
       64.08        13.74         2.89        39.85        30.58        14.73 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52W 
       65.49         3.65        16.80         8.58 

$`22Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
       12.20        75.75        79.46         4.80       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       23.54        92.15        31.99         1.64        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
      154.32        49.94        27.19        99.16        70.16        60.89 
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-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       31.63        41.69        33.93         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
       64.21         1.74        14.10        48.82        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-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        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        54.28        79.20        11.74 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
       30.12        62.86        56.32        16.64        22.06         7.63 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-4589 
      133.74        98.01        79.53       174.08        14.07         1.55 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
       27.02         4.70         0.30       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       27.16         2.63        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.27        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       12.00        16.93        30.94         4.96         1.12        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 
        4.04        26.43        20.91         3.95         0.43         8.12 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        7.82         6.81         0.39        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       70.03        60.79         1.71         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-3394 
       15.58        35.64        35.70        17.88        40.21        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       33.11        18.38        27.91        12.36        24.89        21.47 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        3.81        19.59         7.76        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
       11.61         9.73        14.20        12.03         9.99        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         0.10        18.25         2.04 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
        0.99         0.99         1.45         1.32         0.85         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8308 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
        0.10        17.49        17.00         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.94        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.13         0.26         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-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       35.24        29.92         3.58        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-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       41.42         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       42.64         3.19        32.32        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       26.83        11.77       102.67        70.62        66.61        58.65 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       45.57        14.99        89.29        78.28        16.37        25.41 
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-77-6842 TCGA-77-6843 TCGA-77-6844 
        6.94        13.35        14.73        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       23.28        89.98        20.78         0.49        42.28        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        53.95        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 
       82.92        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         9.63        65.49        35.90 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
        0.33       126.18       132.36       117.57         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 
       42.08        30.81        27.62        38.86         9.67        12.99 
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-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
       29.95        18.94        24.13        31.56        14.07        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         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
       13.94        25.68        19.33        17.72        14.96        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 
       18.18        19.73        12.56        16.21        14.96         0.79 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
        3.65        24.92         9.50         2.93        11.77        14.07 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        2.70         3.48         5.26        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        4.01         5.03        26.63        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       49.87        57.07        18.31        17.46        19.36        16.57 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
       18.15        27.02        21.21        20.32        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD 
       19.10        12.89        16.11        13.18        13.41         0.07 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN 
        4.54        51.78         1.22        45.37         4.21        37.22 
TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52N 
       24.00        29.75        22.78        83.57         0.43        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 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.10               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            151.27             174.08 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            17.605             19.590 
[1] "0.1 - 151.3 (17.6)" "0.0 - 174.1 (19.6)"
[1] "hr=" "1.1"
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         1       16       21        0        17        18
  22Q LOSS WILD-TYPE       1       71      130        2        46        74
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IV
  22Q LOSS MUTATED           0         17          4        2
  22Q LOSS WILD-TYPE         3         45         17        5
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                 16                 71
  STAGE IB                 21                130
  STAGE II                  0                  2
  STAGE IIA                17                 46
  STAGE IIB                18                 74
  STAGE III                 0                  3
  STAGE IIIA               17                 45
  STAGE IIIB                4                 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
  22Q LOSS MUTATED    22  58  15   2
  22Q LOSS WILD-TYPE  89 232  54  21
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               22                 89
  T2               58                232
  T3               15                 54
  T4                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                  N0  N1  N2  N3
  22Q LOSS MUTATED    56  25  13   3
  22Q LOSS WILD-TYPE 256 106  26   2
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               56                256
  N1               25                106
  N2               13                 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"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    77   2
  22Q LOSS WILD-TYPE 327   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     77    2
  22Q LOSS WILD-TYPE  327    5
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               77                327
  1                2                  5
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    24  73
  22Q LOSS WILD-TYPE 103 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24   73
  22Q LOSS WILD-TYPE  103  293
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               24                103
  MALE                 73                293
[1] 2 2
[1] FALSE
D80V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED                                       3
  22Q LOSS WILD-TYPE                                    12
                    vv
clus                 LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED                                         0
  22Q LOSS WILD-TYPE                                       1
                    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                                                            91
  22Q LOSS WILD-TYPE                                                         379
D80V9, multiclass
                                                             clus
vv                                                            22Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               91
                                                             clus
vv                                                            22Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                379
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3  94
  22Q LOSS WILD-TYPE  10 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   94
  22Q LOSS WILD-TYPE   10  386
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 3                 10
  YES               94                386
[1] 2 2
[1] FALSE
D80V11, continuous
D80V12, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    73   4   1   4
  22Q LOSS WILD-TYPE 321   8   3  18
D80V13, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               73                321
  R1                4                  8
  R2                1                  3
  RX                4                 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
  22Q LOSS MUTATED       3                         8    62
  22Q LOSS WILD-TYPE     6                        23   278
D80V14, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                8                 23
  WHITE                                   62                278
[1] 3 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  56
  22Q LOSS WILD-TYPE   6 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   56
  22Q LOSS WILD-TYPE    6  253
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               56                253
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    74  62
  XP LOSS WILD-TYPE 207 134
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              136               341 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               62               134 
$`XP LOSS MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3412 TCGA-18-3416 TCGA-18-3417 TCGA-18-4086 
        7.46        75.75        11.34        31.99        36.07         2.79 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
       49.94        27.19        99.16       122.43       119.80        43.23 
TCGA-22-0940 TCGA-22-4591 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 
       21.99        20.48        19.30        11.77        63.55        44.25 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 
       71.34        79.20        18.84        30.12        56.32        22.06 
TCGA-33-4566 TCGA-33-4582 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ 
      174.08       103.53         0.30        36.62       110.99       118.36 
TCGA-33-AASL TCGA-34-2605 TCGA-34-2609 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
       27.16        28.96        31.27        30.94         4.96         1.12 
TCGA-34-8454 TCGA-34-8456 TCGA-37-4135 TCGA-37-4141 TCGA-39-5021 TCGA-39-5027 
       27.19        26.43         6.81         0.39        68.58        60.79 
TCGA-39-5028 TCGA-39-5037 TCGA-43-5668 TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 
        1.71        35.70        18.38        21.47        19.59        11.77 
TCGA-43-8118 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 
        2.93        10.65         0.39         0.39        29.95        30.35 
TCGA-56-7221 TCGA-56-7222 TCGA-56-8624 TCGA-56-8625 TCGA-56-8629 TCGA-56-A5DR 
        0.99         0.43         1.18        10.36        15.81         0.13 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-60-2696 TCGA-60-2707 
       13.55        29.95        71.24        16.47         3.58        21.93 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2721 TCGA-63-A5MI 
       66.54        41.42         9.01        56.91        32.32        58.65 
TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 
       25.28        16.37        36.16        34.59        16.96         1.02 
TCGA-66-2757 TCGA-66-2763 TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
       43.99         0.99         3.02        12.03         3.98        12.00 
TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2795 TCGA-66-2800 
       25.97         4.04        22.98        30.02         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-77-6842 TCGA-77-6845 TCGA-77-7142 TCGA-77-8009 
        2.73         6.64        29.56        23.28        42.28        53.95 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF 
       11.54        27.39        35.90       117.57        42.08        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-7698 TCGA-85-7699 TCGA-85-8071 TCGA-85-8288 
        9.67        12.99        31.30        32.91        14.07        13.22 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4QR 
        5.29        32.71         0.72        14.63        19.33        19.73 
TCGA-85-A50M TCGA-90-7766 TCGA-92-8063 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
       12.56         9.50         4.01         4.01         5.03        26.63 
TCGA-94-A5I6 TCGA-96-7544 TCGA-98-8020 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J 
       17.69        49.87         2.76        18.15         2.01        20.71 
TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HO 
       13.18         4.54        51.78        45.37         2.89        30.58 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52S TCGA-O2-A5IB 
       65.49        16.80        12.72        11.18 

$`XP LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
       12.20        79.46         4.80       117.57        23.54        92.15 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 
        1.64        86.96         6.18       154.32       119.54        46.88 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
       70.16        60.89        34.78        15.58        31.73         9.34 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
       31.63        88.11        41.69        33.93        10.82        32.19 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
        7.33        14.93         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       27.02        48.82        35.08        48.33        24.13         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-5471 
       38.17        34.75        13.12        32.02         9.57        31.73 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5489 
       64.93        14.63         0.79        54.28        11.74        62.86 
TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 
       16.64         7.63       133.74        98.01        79.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
       14.07        54.44         1.55        19.76        27.02         4.70 
TCGA-33-AASB TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 
        6.94        44.19         2.63        61.61        31.50        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        67.79        56.38         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5928 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       16.93        18.15         4.04        20.91         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 
        0.39         6.58         8.12         7.46         7.82         3.39 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 
       47.80        74.07        44.75        55.20        70.03        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 
        1.94        27.39        36.39        15.58        35.64        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       17.06        40.21        22.49        38.66        27.02        33.11 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 
       27.91        12.36        24.89         5.46         3.81         7.76 
TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
       66.51        13.38        11.61         9.73        14.20        12.03 
TCGA-46-3768 TCGA-46-6026 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
        9.99        13.91        28.34         5.46         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 
       28.96         0.10        18.25         2.04         0.62         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
        1.45         1.32         0.85         6.51         0.10        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
        3.48        26.89        17.00        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW 
        1.81        22.75         9.93        20.25        20.94        19.23 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       13.32        17.85        21.04        18.74         0.26         2.76 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
        0.03        13.25        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-60-2708 TCGA-60-2709 TCGA-60-2714 TCGA-60-2715 
       37.94        92.71        80.45        49.48        50.33        35.34 
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-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ 
       26.83        11.77       102.67        70.62        66.61        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU 
       45.57        14.99        11.34        89.29        78.28        25.41 
TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
       53.88        43.10         2.01        21.07         0.99         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
        0.92         0.99        21.01        25.05         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 
        2.01         2.01         7.07        23.01        19.00         2.01 
TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 
       19.00        24.95         1.97        40.01        22.98         5.03 
TCGA-66-2793 TCGA-66-2794 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
       10.06        54.08         6.94         8.02        13.35        16.18 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 
       14.73        73.12        75.09        11.18        89.98        20.78 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        0.49        70.13       106.95         0.16        46.78        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        6.51        86.76        37.81        82.92        12.59        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
       39.09        17.72       104.09        26.40         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
       54.41        65.49         0.33       126.18       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        5.92        42.41        30.81        38.86        11.97         6.41 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
       36.53        34.95         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        16.87        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 
       10.09         0.76        22.45        16.77         3.09         2.01 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
        7.76        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 
       17.72        14.96        24.36        18.18        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 
       14.96         0.79        12.39         3.65        24.92         2.93 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       11.77        14.07        20.22        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        3.48         5.26         2.30        21.04         0.16        11.70 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       14.14        16.14        57.07        18.31        17.46        19.36 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       16.57         8.42        30.81        30.67        21.34        27.16 
TCGA-98-A539 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH 
        3.88        27.02        21.21        20.32        18.58        19.10 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       12.89        16.11        13.41        11.84         0.07        64.08 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP 
        1.22        13.74         4.21        39.85        37.22        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A7XE 
       14.73        29.75        22.78        83.57         3.65         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       33.07         3.72        43.89         8.58         0.20 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.13              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           174.08            154.32 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            21.09             18.58 
[1] "0.1 - 174.1 (21.1)" "0.0 - 154.3 (18.6)"
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         0       26       40        1        22        26
  XP LOSS WILD-TYPE       2       61      111        1        41        66
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  XP LOSS MUTATED           2         14          7        1
  XP LOSS WILD-TYPE         1         48         14        6
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                26                61
  STAGE IB                40               111
  STAGE II                 1                 1
  STAGE IIA               22                41
  STAGE IIB               26                66
  STAGE III                2                 1
  STAGE IIIA              14                48
  STAGE IIIB               7                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 LOSS MUTATED    37  75  19  10
  XP LOSS WILD-TYPE  74 215  50  13
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              37                74
  T2              75               215
  T3              19                50
  T4              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                 N0  N1  N2  N3
  XP LOSS MUTATED    90  42   7   1
  XP LOSS WILD-TYPE 222  89  32   4
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              90               222
  N1              42                89
  N2               7                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"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   116   1
  XP LOSS WILD-TYPE 288   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    116    1
  XP LOSS WILD-TYPE  288    6
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0             116               288
  1               1                 6
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    38 103
  XP LOSS WILD-TYPE  89 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     38  103
  XP LOSS WILD-TYPE   89  263
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              38                89
  MALE               103               263
[1] 2 2
[1] FALSE
D81V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  XP LOSS MUTATED                                       4
  XP LOSS WILD-TYPE                                    11
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  XP LOSS MUTATED                                         1
  XP LOSS WILD-TYPE                                       0
                   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                                                           134
  XP LOSS WILD-TYPE                                                         336
D81V9, multiclass
                                                             clus
vv                                                            XP LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG CLEAR CELL 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)             134
                                                             clus
vv                                                            XP LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               336
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V10, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     4 137
  XP LOSS WILD-TYPE   9 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      4  137
  XP LOSS WILD-TYPE    9  343
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                4                 9
  YES             137               343
[1] 2 2
[1] FALSE
D81V11, continuous
D81V12, continuous
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED   113   1   0   7
  XP LOSS WILD-TYPE 281  11   4  15
D81V13, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0             113               281
  R1               1                11
  R2               0                 4
  RX               7                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    93
  XP LOSS WILD-TYPE     6                        20   247
D81V14, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              11                20
  WHITE                                  93               247
[1] 3 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  88
  XP LOSS WILD-TYPE   7 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1   88
  XP LOSS WILD-TYPE    7  221
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              88               221
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    53  52
  XQ LOSS WILD-TYPE 228 144
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              105               372 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               52               144 
$`XQ LOSS MUTATED`
TCGA-18-3416 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1080 
       31.99         2.79        49.94        27.19        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-22-A5C4 
       63.55        44.25        79.20        30.12        56.32        22.06 
TCGA-33-4533 TCGA-33-4582 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      133.74       103.53        54.44         4.70         0.30        36.62 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2605 TCGA-34-5929 
      110.99        44.19        27.16        61.61        28.96         4.96 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5027 TCGA-39-5028 TCGA-39-5037 TCGA-43-5668 
        6.81         0.39        60.79         1.71        35.70        18.38 
TCGA-43-7656 TCGA-43-8116 TCGA-46-6025 TCGA-51-4080 TCGA-52-7810 TCGA-56-7221 
       19.59        11.77        10.65         0.39        30.35         0.99 
TCGA-56-7222 TCGA-56-8625 TCGA-56-A5DR TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.43        10.36         0.13        13.55        29.95        71.24 
TCGA-58-8392 TCGA-60-2696 TCGA-60-2712 TCGA-60-2713 TCGA-60-2721 TCGA-60-2726 
       16.47         3.58         9.01        56.91        32.32        11.77 
TCGA-63-A5MI TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2757 TCGA-66-2763 
       58.65        53.88        34.59        16.96        43.99         0.99 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2795 
       12.03        12.00        25.97         4.04        22.98         4.01 
TCGA-68-7755 TCGA-68-7756 TCGA-77-6845 TCGA-77-7142 TCGA-77-8136 TCGA-77-8140 
        2.73         6.64        23.28        42.28        39.09        11.54 
TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-85-6175 TCGA-85-7699 
       27.39        65.49        35.90       117.57         9.67        32.91 
TCGA-85-8071 TCGA-85-8288 TCGA-85-8352 TCGA-85-8479 TCGA-85-8580 TCGA-85-A4QR 
       14.07        13.22         5.29         0.72        14.63        19.73 
TCGA-90-7766 TCGA-92-8063 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 
        9.50         4.01         4.01         5.03        26.63        49.87 
TCGA-98-8022 TCGA-98-A53A TCGA-98-A53B TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HG 
       30.67        18.15         2.01        13.18         4.54        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NK-A5CT 
        1.22        45.37         4.21         2.89        30.58        65.49 
TCGA-NK-A5D1 TCGA-O2-A52S TCGA-O2-A5IB 
       16.80        12.72        11.18 

$`XQ LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       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         1.64        86.96 
TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 
        6.18       154.32       119.54        46.88        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 
       34.78        15.58        31.73         9.34        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 
       41.69        33.93        10.82        32.19         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
        4.31        64.21         1.74        14.10        27.02        48.82 
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-22-5471 TCGA-22-5472 TCGA-22-5474 
       13.12        32.02         9.57        31.73        64.93        14.63 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 
        0.79        54.28        71.34        11.74        18.84        62.86 
TCGA-22-5492 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
       16.64         7.63        98.01        79.53       174.08       151.27 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASB TCGA-33-AASJ 
       14.07         1.55        19.76        27.02         6.94       118.36 
TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
        2.63        31.50        32.88        31.27        65.23        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       56.38         9.07        23.24        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       18.15         1.12        27.19         4.04        26.43        20.91 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        3.95         0.43         0.39         6.58         8.12         7.46 
TCGA-37-4133 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        7.82         3.39        47.80        74.07        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       55.20        70.03        24.33         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
       15.58        35.64        17.88        17.06        40.21        22.49 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       38.66        27.02        33.11        27.91        12.36        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       21.47         5.46         3.81         7.76        66.51        13.38 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
        2.93        11.61         9.73        14.20        12.03         9.99 
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-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
       27.45        28.96         0.10        18.25         2.04         0.62 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.99         1.45         1.32         0.85         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 
       17.49         3.48        26.89        17.00        14.07         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 
       16.77         1.81        22.75         1.18         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
       15.81        20.94        19.23        13.32        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8393 
       18.74         0.26         2.76         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-60-2711 TCGA-60-2714 TCGA-60-2715 
       80.45        49.48        66.54        41.42        50.33        35.34 
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-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML 
       26.83       102.67        70.62        66.61        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-A5MU TCGA-63-A5MV TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       25.41        36.16        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 
        1.02         2.01         0.92         0.99        21.01        25.05 
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-66-2781 TCGA-66-2783 
       19.00         3.02         2.01        19.00         3.98        24.95 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
        1.97        40.01        22.98         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
       54.08        49.05         6.94         8.02        13.35        16.18 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 
       14.73        29.56        73.12        75.09        11.18        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
       20.78         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 
       15.75         6.51        86.76        53.95        37.81        82.92 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 
       12.59        53.92        17.72       104.09        26.40         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
        9.63        54.41         0.33       126.18       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        5.92        42.41        42.08        30.81        27.62        38.86 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       11.97        12.99         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-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       24.13        31.56        16.87        34.52        10.09         0.76 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
       22.45        16.77         3.09        32.71         2.01         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       13.94        12.59         0.10        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z 
       17.72        14.96        24.36        18.18        12.56        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       15.85        14.96         0.79        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        2.93        11.77        14.07        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        2.70         3.48         5.26         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8169 
       11.70        14.14        16.14        17.69        57.07        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 
       17.46        19.36        16.57         8.42         2.76        30.81 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       21.34        27.16         3.88        27.02        21.21        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW 
       18.58        20.71        19.10        12.89        16.11        13.41 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HJ TCGA-NC-A5HM TCGA-NC-A5HN 
       11.84         0.07        64.08        13.74        39.85        37.22 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
       24.00        14.73        29.75        22.78        83.57         3.65 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
        0.43        33.07         3.72        43.89         8.58         0.20 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.13              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           133.74            174.08 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            19.73             19.00 
[1] "0.1 - 133.7 (19.7)" "0.0 - 174.1 (19.0)"
[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       28        0        15        19
  XQ LOSS WILD-TYPE       2       62      123        2        48        73
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IV
  XQ LOSS MUTATED           2         12          6        0
  XQ LOSS WILD-TYPE         1         50         15        7
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                25                62
  STAGE IB                28               123
  STAGE II                 0                 2
  STAGE IIA               15                48
  STAGE IIB               19                73
  STAGE III                2                 1
  STAGE IIIA              12                50
  STAGE IIIB               6                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
  XQ LOSS MUTATED    34  51  15   9
  XQ LOSS WILD-TYPE  77 239  54  14
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              34                77
  T2              51               239
  T3              15                54
  T4               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                 N0  N1  N2  N3
  XQ LOSS MUTATED    70  32   6   1
  XQ LOSS WILD-TYPE 242  99  33   4
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              70               242
  N1              32                99
  N2               6                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"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    87   0
  XQ LOSS WILD-TYPE 317   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     87    0
  XQ LOSS WILD-TYPE  317    7
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              87               317
  1               0                 7
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    33  76
  XQ LOSS WILD-TYPE  94 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     33   76
  XQ LOSS WILD-TYPE   94  290
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              33                94
  MALE                76               290
[1] 2 2
[1] FALSE
D82V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED                                       5
  XQ LOSS WILD-TYPE                                    10
                   vv
clus                LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED                                         0
  XQ LOSS WILD-TYPE                                       1
                   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                                                           102
  XQ LOSS WILD-TYPE                                                         368
D82V9, multiclass
                                                             clus
vv                                                            XQ LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             102
                                                             clus
vv                                                            XQ LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               368
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V10, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3 106
  XQ LOSS WILD-TYPE  10 374
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3  106
  XQ LOSS WILD-TYPE   10  374
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                3                10
  YES             106               374
[1] 2 2
[1] FALSE
D82V11, continuous
D82V12, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    88   1   0   4
  XQ LOSS WILD-TYPE 306  11   4  18
D82V13, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              88               306
  R1               1                11
  R2               0                 4
  RX               4                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       0                         8    77
  XQ LOSS WILD-TYPE     9                        23   263
D82V14, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               8                23
  WHITE                                  77               263
[1] 3 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  67
  XQ LOSS WILD-TYPE   8 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   67
  XQ LOSS WILD-TYPE    8  242
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              67               242
[1] 2 2
[1] FALSE
