[1] "ofn"        "-oTLUAD-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/19775350/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/20217686/transformed.cor.cli.txt"

nPatients in clinical file=521, in cluster file=533, common to both=480
[1]  90 480
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           255            225 
  TP53 MUTATED TP53 WILD-TYPE 
           255            225 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
           150            330 
  KRAS MUTATED KRAS WILD-TYPE 
           150            330 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             84             396 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             84             396 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            67            413 
  EGFR MUTATED EGFR WILD-TYPE 
            67            413 
[1] "STK11 MUTATION ANALYSIS"
[1] 3
  STK11 MUTATED STK11 WILD-TYPE 
             76             404 
  STK11 MUTATED STK11 WILD-TYPE 
             76             404 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
             33             447 
  RBM10 MUTATED RBM10 WILD-TYPE 
             33             447 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           26           454 
  RB1 MUTATED RB1 WILD-TYPE 
           26           454 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              30              450 
  ARID1A MUTATED ARID1A WILD-TYPE 
              30              450 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           55           425 
  NF1 MUTATED NF1 WILD-TYPE 
           55           425 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               38               442 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               38               442 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            38            442 
  BRAF MUTATED BRAF WILD-TYPE 
            38            442 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           40           440 
  MGA MUTATED MGA WILD-TYPE 
           40           440 
[1] "FTSJD1 MUTATION ANALYSIS"
[1] 3
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
              24              456 
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
              24              456 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           21           459 
  MET MUTATED MET WILD-TYPE 
           21           459 
[1] "GAGE2A MUTATION ANALYSIS"
[1] 3
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               8              472 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               8              472 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             30             450 
  SETD2 MUTATED SETD2 WILD-TYPE 
             30             450 
[1] "U2AF1 MUTATION ANALYSIS"
[1] 3
  U2AF1 MUTATED U2AF1 WILD-TYPE 
             11             469 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
             11             469 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             469 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             469 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              464 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              464 
[1] "SRPX MUTATION ANALYSIS"
[1] 3
  SRPX MUTATED SRPX WILD-TYPE 
            14            466 
  SRPX MUTATED SRPX WILD-TYPE 
            14            466 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           42           438 
  ATM MUTATED ATM WILD-TYPE 
           42           438 
[1] "TCEAL5 MUTATION ANALYSIS"
[1] 3
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              13              467 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              13              467 
[1] "PPP3CA MUTATION ANALYSIS"
[1] 3
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              468 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              468 
[1] "FCRLA MUTATION ANALYSIS"
[1] 3
  FCRLA MUTATED FCRLA WILD-TYPE 
             15             465 
  FCRLA MUTATED FCRLA WILD-TYPE 
             15             465 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             24             456 
  ARID2 MUTATED ARID2 WILD-TYPE 
             24             456 
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           20           460 
  APC MUTATED APC WILD-TYPE 
           20           460 
[1] "ZEB1 MUTATION ANALYSIS"
[1] 3
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            32            448 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            32            448 
[1] "SIP1 MUTATION ANALYSIS"
[1] 3
  SIP1 MUTATED SIP1 WILD-TYPE 
             4            476 
  SIP1 MUTATED SIP1 WILD-TYPE 
             4            476 
[1] "SLC4A3 MUTATION ANALYSIS"
[1] 3
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              18              462 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              18              462 
[1] "STK19 MUTATION ANALYSIS"
[1] 3
  STK19 MUTATED STK19 WILD-TYPE 
              5             475 
  STK19 MUTATED STK19 WILD-TYPE 
              5             475 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              475 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              475 
[1] "SLAMF9 MUTATION ANALYSIS"
[1] 3
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
              12              468 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
              12              468 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              18              462 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              18              462 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              461 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              461 
[1] "PTPRU MUTATION ANALYSIS"
[1] 3
  PTPRU MUTATED PTPRU WILD-TYPE 
             18             462 
  PTPRU MUTATED PTPRU WILD-TYPE 
             18             462 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              28              452 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              28              452 
[1] "ZNF608 MUTATION ANALYSIS"
[1] 3
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               9              471 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               9              471 
[1] "STIM1 MUTATION ANALYSIS"
[1] 3
  STIM1 MUTATED STIM1 WILD-TYPE 
              9             471 
  STIM1 MUTATED STIM1 WILD-TYPE 
              9             471 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             5            475 
  EMG1 MUTATED EMG1 WILD-TYPE 
             5            475 
[1] "PHKA1 MUTATION ANALYSIS"
[1] 3
  PHKA1 MUTATED PHKA1 WILD-TYPE 
             12             468 
  PHKA1 MUTATED PHKA1 WILD-TYPE 
             12             468 
[1] "PAK1 MUTATION ANALYSIS"
[1] 3
  PAK1 MUTATED PAK1 WILD-TYPE 
             9            471 
  PAK1 MUTATED PAK1 WILD-TYPE 
             9            471 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             3            477 
  NRAS MUTATED NRAS WILD-TYPE 
             3            477 
[1] "G3BP1 MUTATION ANALYSIS"
[1] 3
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              8             472 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              8             472 
[1] "TRERF1 MUTATION ANALYSIS"
[1] 3
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              18              462 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              18              462 
[1] "CACNA1F MUTATION ANALYSIS"
[1] 3
  CACNA1F MUTATED CACNA1F WILD-TYPE 
               27               453 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
               27               453 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              467 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              467 
[1] "RPL5 MUTATION ANALYSIS"
[1] 3
  RPL5 MUTATED RPL5 WILD-TYPE 
             8            472 
  RPL5 MUTATED RPL5 WILD-TYPE 
             8            472 
[1] "STRA8 MUTATION ANALYSIS"
[1] 3
  STRA8 MUTATED STRA8 WILD-TYPE 
              8             472 
  STRA8 MUTATED STRA8 WILD-TYPE 
              8             472 
[1] "NLRP6 MUTATION ANALYSIS"
[1] 3
  NLRP6 MUTATED NLRP6 WILD-TYPE 
             10             470 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
             10             470 
[1] "FAM65C MUTATION ANALYSIS"
[1] 3
  FAM65C MUTATED FAM65C WILD-TYPE 
              14              466 
  FAM65C MUTATED FAM65C WILD-TYPE 
              14              466 
[1] "WDR66 MUTATION ANALYSIS"
[1] 3
  WDR66 MUTATED WDR66 WILD-TYPE 
             14             466 
  WDR66 MUTATED WDR66 WILD-TYPE 
             14             466 
[1] "RIT1 MUTATION ANALYSIS"
[1] 3
  RIT1 MUTATED RIT1 WILD-TYPE 
             8            472 
  RIT1 MUTATED RIT1 WILD-TYPE 
             8            472 
[1] "TGFBR3 MUTATION ANALYSIS"
[1] 3
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
              14              466 
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
              14              466 
[1] "CXCR7 MUTATION ANALYSIS"
[1] 3
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             10             470 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             10             470 
[1] "GAN MUTATION ANALYSIS"
[1] 3
  GAN MUTATED GAN WILD-TYPE 
           10           470 
  GAN MUTATED GAN WILD-TYPE 
           10           470 
[1] "TMEM49 MUTATION ANALYSIS"
[1] 3
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               5              475 
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               5              475 
[1] "HSPA8 MUTATION ANALYSIS"
[1] 3
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              9             471 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              9             471 
[1] "CD244 MUTATION ANALYSIS"
[1] 3
  CD244 MUTATED CD244 WILD-TYPE 
             12             468 
  CD244 MUTATED CD244 WILD-TYPE 
             12             468 
[1] "KIF18B MUTATION ANALYSIS"
[1] 3
  KIF18B MUTATED KIF18B WILD-TYPE 
               4              476 
  KIF18B MUTATED KIF18B WILD-TYPE 
               4              476 
[1] "PDE6A MUTATION ANALYSIS"
[1] 3
  PDE6A MUTATED PDE6A WILD-TYPE 
             16             464 
  PDE6A MUTATED PDE6A WILD-TYPE 
             16             464 
[1] "CHRND MUTATION ANALYSIS"
[1] 3
  CHRND MUTATED CHRND WILD-TYPE 
             16             464 
  CHRND MUTATED CHRND WILD-TYPE 
             16             464 
[1] "KLK1 MUTATION ANALYSIS"
[1] 3
  KLK1 MUTATED KLK1 WILD-TYPE 
             8            472 
  KLK1 MUTATED KLK1 WILD-TYPE 
             8            472 
[1] "KLHL5 MUTATION ANALYSIS"
[1] 3
  KLHL5 MUTATED KLHL5 WILD-TYPE 
             14             466 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
             14             466 
[1] "DSC2 MUTATION ANALYSIS"
[1] 3
  DSC2 MUTATED DSC2 WILD-TYPE 
            20            460 
  DSC2 MUTATED DSC2 WILD-TYPE 
            20            460 
[1] "RNF160 MUTATION ANALYSIS"
[1] 3
  RNF160 MUTATED RNF160 WILD-TYPE 
              15              465 
  RNF160 MUTATED RNF160 WILD-TYPE 
              15              465 
[1] "AIFM1 MUTATION ANALYSIS"
[1] 3
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             12             468 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             12             468 
[1] "DOT1L MUTATION ANALYSIS"
[1] 3
  DOT1L MUTATED DOT1L WILD-TYPE 
             14             466 
  DOT1L MUTATED DOT1L WILD-TYPE 
             14             466 
[1] "MCM9 MUTATION ANALYSIS"
[1] 3
  MCM9 MUTATED MCM9 WILD-TYPE 
             3            477 
  MCM9 MUTATED MCM9 WILD-TYPE 
             3            477 
[1] "NCKAP1L MUTATION ANALYSIS"
[1] 3
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
               19               461 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
               19               461 
[1] "ESYT3 MUTATION ANALYSIS"
[1] 3
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              8             472 
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              8             472 
[1] "MIA2 MUTATION ANALYSIS"
[1] 3
  MIA2 MUTATED MIA2 WILD-TYPE 
            13            467 
  MIA2 MUTATED MIA2 WILD-TYPE 
            13            467 
[1] "TUBB4 MUTATION ANALYSIS"
[1] 3
  TUBB4 MUTATED TUBB4 WILD-TYPE 
             17             463 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
             17             463 
[1] "ABHD12B MUTATION ANALYSIS"
[1] 3
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                7               473 
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                7               473 
[1] "ANTXR1 MUTATION ANALYSIS"
[1] 3
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              19              461 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              19              461 
[1] "FLCN MUTATION ANALYSIS"
[1] 3
  FLCN MUTATED FLCN WILD-TYPE 
             9            471 
  FLCN MUTATED FLCN WILD-TYPE 
             9            471 
[1] "ZNF556 MUTATION ANALYSIS"
[1] 3
  ZNF556 MUTATED ZNF556 WILD-TYPE 
              12              468 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
              12              468 
[1] "ASCL3 MUTATION ANALYSIS"
[1] 3
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              7             473 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              7             473 
[1] "DSG3 MUTATION ANALYSIS"
[1] 3
  DSG3 MUTATED DSG3 WILD-TYPE 
            33            447 
  DSG3 MUTATED DSG3 WILD-TYPE 
            33            447 
[1] "C5AR1 MUTATION ANALYSIS"
[1] 3
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              5             475 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              5             475 
[1] "ASXL2 MUTATION ANALYSIS"
[1] 3
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             18             462 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             18             462 
[1] "DLX5 MUTATION ANALYSIS"
[1] 3
  DLX5 MUTATED DLX5 WILD-TYPE 
            13            467 
  DLX5 MUTATED DLX5 WILD-TYPE 
            13            467 
[1] "ATAD2 MUTATION ANALYSIS"
[1] 3
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             14             466 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             14             466 
[1] "RAF1 MUTATION ANALYSIS"
[1] 3
  RAF1 MUTATED RAF1 WILD-TYPE 
             6            474 
  RAF1 MUTATED RAF1 WILD-TYPE 
             6            474 
[1] "A2M MUTATION ANALYSIS"
[1] 3
  A2M MUTATED A2M WILD-TYPE 
           20           460 
  A2M MUTATED A2M WILD-TYPE 
           20           460 
[1] "SND1 MUTATION ANALYSIS"
[1] 3
  SND1 MUTATED SND1 WILD-TYPE 
            16            464 
  SND1 MUTATED SND1 WILD-TYPE 
            16            464 
[1] "C7ORF36 MUTATION ANALYSIS"
[1] 3
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
                6               474 
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
                6               474 
[1] "HTRA1 MUTATION ANALYSIS"
[1] 3
  HTRA1 MUTATED HTRA1 WILD-TYPE 
             10             470 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
             10             470 
[1] "ADAMTS2 MUTATION ANALYSIS"
[1] 3
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
               39               441 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
               39               441 
[1] "TAF1L MUTATION ANALYSIS"
[1] 3
  TAF1L MUTATED TAF1L WILD-TYPE 
             50             430 
  TAF1L MUTATED TAF1L WILD-TYPE 
             50             430 
[1] "PLEKHB2 MUTATION ANALYSIS"
[1] 3
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               474 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               474 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RESIDUAL_TUMOR"                      
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 480 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=148,	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=303,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=91,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 480 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "KARNOFSKY_PERFORMANCE_SCORE"  
 [9] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RESIDUAL_TUMOR"               
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=49, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=8, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
155 261  43  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
155 261  43  18 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
155 261  43  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
155 261  43  18 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
307  89  70   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  307    89    72 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
307  89  70   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  307    89    72 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=11, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=91, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=57, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   160  86
  TP53 WILD-TYPE 142  69
  TP53 MUTATED TP53 WILD-TYPE 
           246            211 
  TP53 MUTATED TP53 WILD-TYPE 
            86             69 
$`TP53 MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 
       19.96        14.01         0.00         9.96        24.03        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4426 
        8.02        20.05         2.99        29.98        30.02        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4629 
       22.03         7.40         5.98         8.68        97.74        28.41 
TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-3396 TCGA-44-3918 
       35.28        44.61        14.73        46.98        37.15        34.06 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 
       33.30        28.37        28.01        23.77        19.56        27.78 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       21.63        23.18        32.45        61.28        16.44        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 
       12.03         7.17        36.07        18.87        29.00        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 
        8.55        15.98        11.54        13.64        13.45        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4514 TCGA-49-6767 TCGA-50-5045 
       28.57        12.66        14.07        55.89        22.26        71.47 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       70.55        31.04        49.28         9.27        14.27        78.67 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       15.12         9.37        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8460 
       25.55        11.05        12.16         6.21         0.72        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6712 
       34.29        30.54        35.21        23.05         2.86         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6975 TCGA-55-6979 TCGA-55-6985 TCGA-55-7227 
       42.51        40.73         3.88         7.79        40.54         1.74 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        1.15         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.28         1.12        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
        6.15        19.82         0.16        29.72         3.29         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        0.13        23.64         1.08        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
        0.76         0.36         0.26        17.72         0.30         6.64 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
       17.62         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       21.40        20.58         0.92        20.19        19.99         4.57 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46U TCGA-62-A46Y 
       88.64        49.25        47.80        56.71        67.96        13.61 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5775 TCGA-64-5778 TCGA-67-3771 TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 
        2.04        42.90        20.05         6.64         5.42         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-8520 
        4.41         2.93        12.56         4.24        17.16         6.90 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
       26.30         4.31         9.24        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 
        5.69        19.27       129.53        21.90        19.50        38.50 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
       26.53        31.20         8.02        39.35        10.55       232.18 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        27.09         5.88        31.13        34.39 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       32.78        19.89         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8672 
       22.82        31.20        23.05        21.47         1.15         0.62 
TCGA-86-8673 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6831 TCGA-91-6836 
       28.34        24.23        13.64        41.36        10.19        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 
       12.23        27.68         7.36         1.18         1.45         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        41.82        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 
       18.67        12.39        15.68        27.29         2.76        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 
       25.48         5.95         0.59        17.92        18.12        14.30 
TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-7458 TCGA-99-8025 
       21.60        20.19        21.44        19.76        24.56        34.85 
TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N1 
       36.76        21.57        18.08        19.00        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TA 
       38.63         2.76        86.14        86.04        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J 
        2.43        11.05        14.10        19.13        71.05        59.11 

$`TP53 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4403 TCGA-05-4417 
       50.07         3.98        45.01        37.02        19.00        14.96 
TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4434 TCGA-05-5420 TCGA-05-5429 
        9.01        12.00        21.99        15.02        15.02         9.04 
TCGA-05-5715 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-38-7271 
        2.04       120.79        37.71        49.05        11.64        26.30 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3398 TCGA-44-3919 
        4.37        44.42        38.10        42.77        38.24        33.73 
TCGA-44-4112 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-7659 TCGA-44-7671 
       26.56         9.93        23.15        63.72        22.72        29.23 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-49-4486 
       13.74         3.25        15.32         9.44        11.08        76.21 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        46.72        32.84         8.81        29.46        29.75 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 
       16.04        53.29        55.33        17.16        11.64        20.52 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 
       15.72        60.16         8.09        40.60        21.47         8.45 
TCGA-50-5942 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-53-7813 
       29.03        41.69        10.13        36.99         7.59        13.94 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       48.62         0.07        32.65        15.25         0.82        48.49 
TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        5.49         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7725 TCGA-55-7728 
      107.21        70.26         0.59         7.99         1.28         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 
        1.78         1.45        15.19        19.66        19.73        15.65 
TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 
       17.98         1.51         2.17         0.95         0.49         0.10 
TCGA-55-8513 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 
        4.80         0.49        20.71         1.58        19.59        15.81 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46V 
       39.98        42.38        14.60        19.53        54.35        72.30 
TCGA-62-A470 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
       39.25        87.98        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 
       14.04        14.73         5.72         4.64        13.87         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 
       22.68        13.61         7.56        14.01        13.45         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4677 
       52.60        23.38        82.68        15.35        30.31         1.25 
TCGA-73-7498 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
       39.09        20.58        39.95       119.51        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       88.14        53.33        26.01        50.24        39.75        77.59 
TCGA-86-6562 TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8076 
       12.36        38.04        20.55        35.24        37.74        32.65 
TCGA-86-8278 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 
       31.04        14.60        13.91        30.84        27.58        26.50 
TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6849 
       29.46        26.47        10.62         1.97         2.60         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.18        16.60        14.27        19.82        22.45        17.46 
TCGA-93-A4JQ TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       17.29        15.65        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 
       64.60        63.52         0.72        18.67         5.39        15.39 
TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       16.41        20.58        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
       20.68         1.45        24.30        23.80        35.47        32.48 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
       14.30         6.35        58.45        49.35        37.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 
        5.49         5.29        10.09        29.46        24.36        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R 
       19.82 

  TP53 MUTATED TP53 WILD-TYPE 
          0.00           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
        232.18         238.29 
  TP53 MUTATED TP53 WILD-TYPE 
         19.53          19.89 
[1] "0.0 - 232.2 (19.5)" "0.1 - 238.3 (19.9)"
[1] "hr=" "1.3"
D1V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TP53 MUTATED         3       61       73        24        35         36
  TP53 WILD-TYPE       1       62       59        23        31         34
                vv
clus             STAGE IIIB STAGE IV
  TP53 MUTATED            8       15
  TP53 WILD-TYPE          3       10
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I               3              1
  STAGE IA             61             62
  STAGE IB             73             59
  STAGE IIA            24             23
  STAGE IIB            35             31
  STAGE IIIA           36             34
  STAGE IIIB            8              3
  STAGE IV             15             10
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TP53 MUTATED    79 142  20  12
  TP53 WILD-TYPE  76 119  23   6
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           79             76
  T2          142            119
  T3           20             23
  T4           12              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1 N2+N3
  TP53 MUTATED   164  47    38
  TP53 WILD-TYPE 143  42    34
D1V5, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  N0             164            143
  N1              47             42
  N2+N3           38             34
[1] 3 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
  TP53 MUTATED   166  14
  TP53 WILD-TYPE 162   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    166   14
  TP53 WILD-TYPE  162    9
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          166            162
  1           14              9
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED   138 117
  TP53 WILD-TYPE 121 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    138  117
  TP53 WILD-TYPE  121  104
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE          138            121
  MALE            117            104
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus               0   1
  TP53 MUTATED   166  35
  TP53 WILD-TYPE 167  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    166   35
  TP53 WILD-TYPE  167   14
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           166            167
  YES           35             14
[1] 2 2
[1] FALSE
D1V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TP53 MUTATED                            8                                51
  TP53 WILD-TYPE                         10                                50
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                  172
  TP53 WILD-TYPE                                                123
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TP53 MUTATED                                            1
  TP53 WILD-TYPE                                          3
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TP53 MUTATED                                              11
  TP53 WILD-TYPE                                             8
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  TP53 MUTATED                                0
  TP53 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  TP53 MUTATED                                    1
  TP53 WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TP53 MUTATED                              0                             7
  TP53 WILD-TYPE                            2                            15
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TP53 MUTATED                                               3
  TP53 WILD-TYPE                                             2
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  TP53 MUTATED                              1
  TP53 WILD-TYPE                            8
D1V10, multiclass
                                                    clus
vv                                                   TP53 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          172
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                11
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 7
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 3
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   TP53 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            123
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   8
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  15
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   2
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
D1V12, continuous
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   163   5   1  14
  TP53 WILD-TYPE 147   6   3  11
D1V13, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          163            147
  R1            5              6
  R2            1              3
  RX           14             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  0     3
  TP53 WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          22   197
  TP53 WILD-TYPE                         7   180
D1V14, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              4
  BLACK OR AFRICAN AMERICAN                  22              7
  WHITE                                     197            180
[1] 4 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
  TP53 MUTATED     6 188
  TP53 WILD-TYPE   0 161
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      6  188
  TP53 WILD-TYPE    0  161
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                6              0
  NOT HISPANIC OR LATINO          188            161
[1] 2 2
[1] FALSE

Clustering(2) Variable = KRAS MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  KRAS MUTATED    96  48
  KRAS WILD-TYPE 206 107
  KRAS MUTATED KRAS WILD-TYPE 
           144            313 
  KRAS MUTATED KRAS WILD-TYPE 
            48            107 
$`KRAS MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4403 TCGA-05-4415 
       50.07         3.98        37.02         0.00        19.00         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4427 TCGA-05-4433 TCGA-38-4626 TCGA-44-6145 
       14.96         9.01        26.01        24.00       120.79        19.56 
TCGA-44-6146 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 
        9.93        63.72        32.45        22.72        12.03        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A47A TCGA-44-A47F TCGA-49-4505 TCGA-49-4510 
       13.74        12.66        15.32        11.08        14.07        29.46 
TCGA-49-6761 TCGA-50-5051 TCGA-50-5932 TCGA-50-5941 TCGA-50-8457 TCGA-50-8459 
       11.64        15.72        40.60         9.37        36.99         7.59 
TCGA-53-7813 TCGA-55-1595 TCGA-55-6642 TCGA-55-6970 TCGA-55-6975 TCGA-55-6983 
       13.94        48.62        32.65        15.25         3.88        60.03 
TCGA-55-6984 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7725 
       24.99         0.59         1.15         7.99         1.32         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.28         0.79         1.78         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8207 
        6.15        19.66         0.13        15.65        17.98         2.17 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8508 TCGA-55-8512 TCGA-55-8514 TCGA-55-8615 
       15.42         0.76         0.49         0.10         6.64         0.49 
TCGA-55-8616 TCGA-55-A490 TCGA-55-A494 TCGA-62-8398 TCGA-62-A46R TCGA-62-A46S 
        1.58         1.58        15.81        14.60        56.71        54.35 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3773 TCGA-67-4679 
       87.98         2.04        42.90        28.47        14.04        14.73 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         4.41        12.56        14.01        13.45 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-78-7145 
       23.38        82.68         4.31         1.25        39.09        27.16 
TCGA-78-7148 TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 TCGA-78-7167 TCGA-78-7539 
       20.58        22.92         9.57         8.48        88.14        26.01 
TCGA-78-7540 TCGA-78-8655 TCGA-83-5908 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 
       39.35        77.59        27.09        38.04        32.78        37.74 
TCGA-86-8056 TCGA-86-8076 TCGA-86-8359 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
        4.57        32.65        14.60        26.50        29.46        24.23 
TCGA-91-6828 TCGA-91-6836 TCGA-91-8497 TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JO 
       10.62        13.71        14.27        22.45         6.12         1.08 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       41.82         2.86        18.67        21.40        18.18        19.89 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8176 TCGA-97-8179 TCGA-97-A4M0 
       25.48         0.59         0.72        15.39        14.30        21.44 
TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.84        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8194 TCGA-J2-A4AG TCGA-L9-A443 TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T4 
       23.80        32.48         6.35         2.76        49.35        86.04 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
        5.49         5.29        10.09        29.46        11.05        14.10 
TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55O TCGA-NJ-A55R 
       19.13        62.60         0.13         1.64         0.43        19.82 

$`KRAS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 
       19.96        14.01        45.01         9.96        24.03        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        8.02        20.05        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       26.01        25.02        25.02        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        8.68        97.74        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       11.64        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       44.42        38.10        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 
       27.78        23.15        21.63        23.18        61.28        16.44 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8119 
       19.46         7.17        36.07        18.87        29.00         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
        8.55        15.98         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       32.84         8.81        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       55.33        17.16        22.26        20.52        71.47        70.55 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
       78.67        21.47         8.45        15.12        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
        6.21        41.69         0.72        10.13        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
       30.54        35.21        23.05         2.86         0.07         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 
       42.51        40.73         0.82        48.49         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        2.20        45.34        32.71        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7727 
        1.74         0.20         0.13         3.12        23.18         1.12 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        1.45        18.64        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
        3.29        19.73         5.06        23.64         1.08         1.51 
TCGA-55-8208 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
       22.16         1.45         0.95         0.36         0.26        17.72 
TCGA-55-8511 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        0.30         4.80        17.62         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       22.65        20.71        21.40        20.58        19.59         0.92 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
       20.19        19.99         4.57        39.98        42.38        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       49.25        47.80        19.53        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 
       38.37        28.41        51.25        20.05        18.84         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
        5.42         2.93         4.24        17.16         2.01         6.90 
TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
       52.60        26.30        15.35        30.31         9.24        50.33 
TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      163.10         5.69        19.27       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      104.19       238.29        26.53        31.20         8.02        53.33 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
       10.55        50.24       232.18        39.75        10.55       110.50 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
       12.36         5.88        31.13        34.39        20.55        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 
       35.24         4.08        24.33         0.79        22.82        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.20        23.05        21.47         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       27.58         0.62        28.34        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.18        16.60         1.18         1.45        19.82 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7944 
       17.46        23.61        19.00        17.29        16.54        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 
       15.68        15.65        27.29         2.76        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       63.52        43.79         5.95        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 
       18.12        16.41        21.60        20.58        20.19        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD 
       20.52        17.75        18.67        20.68        24.30        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       35.47        19.00        14.30        10.09        27.19        38.63 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.14        58.45        37.35        58.85        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55A 
        2.43        24.36        73.91        71.05        29.13         0.26 
TCGA-O1-A52J 
       59.11 

  KRAS MUTATED KRAS WILD-TYPE 
          0.00           0.07 
  KRAS MUTATED KRAS WILD-TYPE 
        120.79         238.29 
  KRAS MUTATED KRAS WILD-TYPE 
        15.105         20.680 
[1] "0.0 - 120.8 (15.1)" "0.1 - 238.3 (20.7)"
[1] "hr=" "1.3"
D2V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KRAS MUTATED         1       37       33        16        25         24
  KRAS WILD-TYPE       3       86       99        31        41         46
                vv
clus             STAGE IIIB STAGE IV
  KRAS MUTATED            3        9
  KRAS WILD-TYPE          8       16
D2V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I               1              3
  STAGE IA             37             86
  STAGE IB             33             99
  STAGE IIA            16             31
  STAGE IIB            25             41
  STAGE IIIA           24             46
  STAGE IIIB            3              8
  STAGE IV              9             16
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KRAS MUTATED    42  82  17   8
  KRAS WILD-TYPE 113 179  26  10
D2V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1           42            113
  T2           82            179
  T3           17             26
  T4            8             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
  KRAS MUTATED    94  30    23
  KRAS WILD-TYPE 213  59    49
D2V5, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  N0              94            213
  N1              30             59
  N2+N3           23             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                cls
clus               0   1
  KRAS MUTATED    98   9
  KRAS WILD-TYPE 230  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     98    9
  KRAS WILD-TYPE  230   14
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           98            230
  1            9             14
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  KRAS MUTATED    81  69
  KRAS WILD-TYPE 178 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     81   69
  KRAS WILD-TYPE  178  152
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           81            178
  MALE             69            152
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus               0   1
  KRAS MUTATED   107   9
  KRAS WILD-TYPE 226  40
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    107    9
  KRAS WILD-TYPE  226   40
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO           107            226
  YES            9             40
[1] 2 2
[1] FALSE
D2V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KRAS MUTATED                            6                                32
  KRAS WILD-TYPE                         12                                69
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KRAS MUTATED                                                   85
  KRAS WILD-TYPE                                                210
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KRAS MUTATED                                            1
  KRAS WILD-TYPE                                          3
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KRAS MUTATED                                               8
  KRAS WILD-TYPE                                            11
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  KRAS MUTATED                                1
  KRAS WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  KRAS MUTATED                                    0
  KRAS WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KRAS MUTATED                              1                            10
  KRAS WILD-TYPE                            1                            12
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KRAS MUTATED                                               1
  KRAS WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  KRAS MUTATED                              5
  KRAS WILD-TYPE                            4
D2V10, multiclass
                                                    clus
vv                                                   KRAS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           85
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 8
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                10
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  5
                                                    clus
vv                                                   KRAS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            210
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  11
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                  12
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
D2V12, continuous
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED    98   3   2   8
  KRAS WILD-TYPE 212   8   2  17
D2V13, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           98            212
  R1            3              8
  R2            2              2
  RX            8             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  0     3
  KRAS WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED                          11   114
  KRAS WILD-TYPE                        18   263
D2V14, multiclass
                                  clus
vv                                 KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              4
  BLACK OR AFRICAN AMERICAN                  11             18
  WHITE                                     114            263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                cls
clus               0   1
  KRAS MUTATED     0 108
  KRAS WILD-TYPE   6 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0  108
  KRAS WILD-TYPE    6  241
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO          108            241
[1] 2 2
[1] FALSE

Clustering(3) Variable = KEAP1 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  KEAP1 MUTATED    45  35
  KEAP1 WILD-TYPE 257 120
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             80             377 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             35             120 
$`KEAP1 MUTATED`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4418 TCGA-35-5375 TCGA-38-4631 
       14.01        45.01         0.00         9.01         8.68        11.64 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       63.72        61.28        16.44        19.46        36.07        18.87 
TCGA-44-7671 TCGA-44-A47F TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 TCGA-49-4506 
       29.23        11.08        13.64        76.21        28.57        32.84 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-50-5051 TCGA-50-5068 
        8.81        55.89        16.04        53.29        15.72        49.28 
TCGA-50-5936 TCGA-50-5939 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6970 
        8.45        15.12        34.29        35.21         2.86        15.25 
TCGA-55-6972 TCGA-55-6987 TCGA-55-7815 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 
       48.49        70.26         1.78         0.16        29.72         0.13 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8620 TCGA-55-A492 
        0.76         0.95         0.36        17.72         2.17        19.59 
TCGA-55-A4DF TCGA-62-8398 TCGA-62-A46O TCGA-62-A470 TCGA-64-5781 TCGA-67-3771 
       20.19        14.60        47.80        39.25        51.25        20.05 
TCGA-69-8253 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       14.01        26.30         4.31         9.24         1.25        39.09 
TCGA-78-7146 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
        5.69       129.53       119.51        19.50        32.09         5.88 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7633 TCGA-86-8358 TCGA-86-8674 
      104.19         8.48        88.14        50.24        21.47        26.50 
TCGA-91-6848 TCGA-91-6849 TCGA-95-7043 TCGA-95-7947 TCGA-97-8176 TCGA-97-8179 
        7.36         1.15        16.54        15.68        15.39        14.30 
TCGA-97-A4M3 TCGA-99-8033 TCGA-J2-8194 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A5C7 
       17.75        21.57        23.80         5.49        29.46        73.91 
TCGA-NJ-A4YQ TCGA-NJ-A55R 
       29.13        19.82 

$`KEAP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4390 TCGA-05-4396 TCGA-05-4397 
       50.07         3.98        19.96        37.02         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       47.05         8.02        19.00        20.05         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       29.98        12.00        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
        9.93        27.78        23.15        21.63        23.18        32.45 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
       22.72        12.03         7.17        29.00        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
        3.25         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       13.45        28.11        12.66        35.54        46.72        14.07 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       29.46        29.75        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
       20.52        71.47        70.55        60.16        31.04         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
        9.27        14.27        40.60        78.67        21.47         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 
       36.99         7.59        27.25        30.54        13.94        23.05 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       48.62         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
        0.82         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 
       32.71        60.03        24.99        40.54       107.21         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       19.82        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 
       22.16        15.42         1.45         0.26         0.49         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.61        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       20.58         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       42.38        88.64        49.25        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       67.96        72.30        13.61        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       28.41        28.47        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41         2.93        12.56 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 TCGA-78-7143 
       23.38        82.68        15.35        30.31        50.33       163.10 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 
       27.16        19.27        20.58        21.90        39.95        38.50 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 
       64.90        22.92         9.57       238.29        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       28.34        29.46        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
       27.68        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29        41.82         2.86        18.67        12.39 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       20.52        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        24.30        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        24.36        14.10        19.13        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.13         1.64         0.26         0.43        59.11 

  KEAP1 MUTATED KEAP1 WILD-TYPE 
           0.00            0.07 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
         129.53          238.29 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
         19.165          19.890 
[1] "0.0 - 129.5 (19.2)" "0.1 - 238.3 (19.9)"
[1] "hr=" "1.2"
D3V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KEAP1 MUTATED         0       24       18         7         8         15
  KEAP1 WILD-TYPE       4       99      114        40        58         55
                 vv
clus              STAGE IIIB STAGE IV
  KEAP1 MUTATED            3        9
  KEAP1 WILD-TYPE          8       16
D3V3, multiclass
            clus
vv           KEAP1 MUTATED KEAP1 WILD-TYPE
  STAGE I                0               4
  STAGE IA              24              99
  STAGE IB              18             114
  STAGE IIA              7              40
  STAGE IIB              8              58
  STAGE IIIA            15              55
  STAGE IIIB             3               8
  STAGE IV               9              16
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KEAP1 MUTATED    29  43   7   4
  KEAP1 WILD-TYPE 126 218  36  14
D3V4, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  T1            29             126
  T2            43             218
  T3             7              36
  T4             4              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
  KEAP1 MUTATED    51  16    15
  KEAP1 WILD-TYPE 256  73    57
D3V5, multiclass
       clus
vv      KEAP1 MUTATED KEAP1 WILD-TYPE
  N0               51             256
  N1               16              73
  N2+N3            15              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                 cls
clus                0   1
  KEAP1 MUTATED    50   9
  KEAP1 WILD-TYPE 278  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     50    9
  KEAP1 WILD-TYPE  278   14
   clus
vv  KEAP1 MUTATED KEAP1 WILD-TYPE
  0            50             278
  1             9              14
[1] 2 2
[1] FALSE
D3V7, binary
                 cls
clus                0   1
  KEAP1 MUTATED    36  48
  KEAP1 WILD-TYPE 223 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     36   48
  KEAP1 WILD-TYPE  223  173
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  FEMALE            36             223
  MALE              48             173
[1] 2 2
[1] FALSE
D3V8, binary
                 cls
clus                0   1
  KEAP1 MUTATED    55  12
  KEAP1 WILD-TYPE 278  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     55   12
  KEAP1 WILD-TYPE  278   37
     clus
vv    KEAP1 MUTATED KEAP1 WILD-TYPE
  NO             55             278
  YES            12              37
[1] 2 2
[1] FALSE
D3V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KEAP1 MUTATED                            4                                20
  KEAP1 WILD-TYPE                         14                                81
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KEAP1 MUTATED                                                   50
  KEAP1 WILD-TYPE                                                245
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KEAP1 MUTATED                                            0
  KEAP1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KEAP1 MUTATED                                               1
  KEAP1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  KEAP1 MUTATED                                1
  KEAP1 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  KEAP1 MUTATED                                    0
  KEAP1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KEAP1 MUTATED                              0                             6
  KEAP1 WILD-TYPE                            2                            16
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KEAP1 MUTATED                                               0
  KEAP1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  KEAP1 MUTATED                              2
  KEAP1 WILD-TYPE                            7
D3V10, multiclass
                                                    clus
vv                                                   KEAP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            50
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  6
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   2
                                                    clus
vv                                                   KEAP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             245
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   16
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
D3V12, continuous
                 vv
clus               R0  R1  R2  RX
  KEAP1 MUTATED    54   3   0   4
  KEAP1 WILD-TYPE 256   8   4  21
D3V13, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  R0            54             256
  R1             3               8
  R2             0               4
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KEAP1 MUTATED                                  0     0
  KEAP1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KEAP1 MUTATED                           6    69
  KEAP1 WILD-TYPE                        23   308
D3V14, multiclass
                                  clus
vv                                 KEAP1 MUTATED KEAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    6              23
  WHITE                                       69             308
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                 cls
clus                0   1
  KEAP1 MUTATED     2  56
  KEAP1 WILD-TYPE   4 293
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      2   56
  KEAP1 WILD-TYPE    4  293
                        clus
vv                       KEAP1 MUTATED KEAP1 WILD-TYPE
  HISPANIC OR LATINO                 2               4
  NOT HISPANIC OR LATINO            56             293
[1] 2 2
[1] FALSE

Clustering(4) Variable = EGFR MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  EGFR MUTATED    36  27
  EGFR WILD-TYPE 266 128
  EGFR MUTATED EGFR WILD-TYPE 
            63            394 
  EGFR MUTATED EGFR WILD-TYPE 
            27            128 
$`EGFR MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-5423 TCGA-05-5425 TCGA-38-4627 TCGA-38-4628 
       19.96         8.02         4.96        29.00        37.71        49.05 
TCGA-38-4629 TCGA-38-6178 TCGA-44-2661 TCGA-44-6147 TCGA-44-A4SU TCGA-49-4490 
       28.41        14.73        38.10        27.78        13.45        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-50-5066 TCGA-50-5944 TCGA-50-6591 TCGA-50-6595 
       35.54        46.72        31.04        25.12         3.91         6.21 
TCGA-50-6673 TCGA-55-6968 TCGA-55-6980 TCGA-55-6981 TCGA-55-7570 TCGA-55-7573 
        0.72        42.51         2.20        45.34         0.20         0.13 
TCGA-55-8096 TCGA-55-8206 TCGA-55-8506 TCGA-55-A48Z TCGA-62-8394 TCGA-62-8402 
       23.64         1.51         0.36        21.40         4.57        49.25 
TCGA-62-A46U TCGA-64-1681 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 
       67.96        38.37        18.84        13.87         6.64         5.42 
TCGA-71-8520 TCGA-78-7147 TCGA-78-7155 TCGA-78-7158 TCGA-86-8055 TCGA-86-8074 
        6.90        19.27        38.50         5.88         4.08         0.79 
TCGA-86-8075 TCGA-86-8280 TCGA-86-8668 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6835 
       22.82        23.05        13.91        24.23        13.64         2.60 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7947 TCGA-97-8171 TCGA-97-8172 TCGA-97-8177 
       19.00        41.82        15.68        18.67        17.92        16.41 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-J2-8192 
       21.60        20.58        19.76        18.67        20.68        24.30 
TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4T9 
       58.45        58.85        41.59 

$`EGFR WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03        47.05        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       15.02        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        8.68        97.74       120.79        35.28        11.64        44.61 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        46.98        44.42        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 
       28.01        23.77        19.56         9.93        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.23        13.74        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       15.32         9.44        11.08        11.54        13.64        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       28.11        28.57        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 
       22.55        42.35        25.55        11.05        12.16        41.69 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94        35.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       32.65         0.79        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88         5.49         7.79        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.99         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65        17.98         1.08         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O 
       19.99        39.98        42.38        14.60        88.64        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        54.35        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-5774 
       40.96        29.92        56.81        20.65        81.80        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
       14.04        14.73         5.72         4.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         7.56         6.05         4.41         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
       14.01        13.45         4.24        17.16         2.01        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       19.50        32.09        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
       19.89        35.24        37.74         4.57        24.33        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
       31.04        31.20        21.47        14.60         1.15        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P8 
       27.58         0.62        28.34        26.50        29.46        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36         1.97        10.19        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       23.61         1.08        17.29        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        5.95         0.59         0.72         5.39        18.12        15.39 
TCGA-97-8179 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       14.30        20.19        21.44        20.52        17.75        20.84 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
       24.56        34.85        36.76         1.45        21.57        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY 
       10.09        27.19        38.63         2.76        86.14        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       37.35        86.04         5.49         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  EGFR MUTATED EGFR WILD-TYPE 
          0.13           0.00 
  EGFR MUTATED EGFR WILD-TYPE 
         67.96         238.29 
  EGFR MUTATED EGFR WILD-TYPE 
         19.27          19.82 
[1] "0.1 - 68.0 (19.3)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.6"
D4V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  EGFR MUTATED         2       15       13         7        11         10
  EGFR WILD-TYPE       2      108      119        40        55         60
                vv
clus             STAGE IIIB STAGE IV
  EGFR MUTATED            3        6
  EGFR WILD-TYPE          8       19
D4V3, multiclass
            clus
vv           EGFR MUTATED EGFR WILD-TYPE
  STAGE I               2              2
  STAGE IA             15            108
  STAGE IB             13            119
  STAGE IIA             7             40
  STAGE IIB            11             55
  STAGE IIIA           10             60
  STAGE IIIB            3              8
  STAGE IV              6             19
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EGFR MUTATED    23  33   7   3
  EGFR WILD-TYPE 132 228  36  15
D4V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1           23            132
  T2           33            228
  T3            7             36
  T4            3             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
  EGFR MUTATED    38  12    14
  EGFR WILD-TYPE 269  77    58
D4V5, multiclass
       clus
vv      EGFR MUTATED EGFR WILD-TYPE
  N0              38            269
  N1              12             77
  N2+N3           14             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                cls
clus               0   1
  EGFR MUTATED    48   5
  EGFR WILD-TYPE 280  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     48    5
  EGFR WILD-TYPE  280   18
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0           48            280
  1            5             18
[1] 2 2
[1] FALSE
D4V7, binary
                cls
clus               0   1
  EGFR MUTATED    44  23
  EGFR WILD-TYPE 215 198
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     44   23
  EGFR WILD-TYPE  215  198
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE           44            215
  MALE             23            198
[1] 2 2
[1] FALSE
D4V8, binary
                cls
clus               0   1
  EGFR MUTATED    46   8
  EGFR WILD-TYPE 287  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     46    8
  EGFR WILD-TYPE  287   41
     clus
vv    EGFR MUTATED EGFR WILD-TYPE
  NO            46            287
  YES            8             41
[1] 2 2
[1] FALSE
D4V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  EGFR MUTATED                            3                                18
  EGFR WILD-TYPE                         15                                83
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  EGFR MUTATED                                                   39
  EGFR WILD-TYPE                                                256
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  EGFR MUTATED                                            1
  EGFR WILD-TYPE                                          3
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  EGFR MUTATED                                               3
  EGFR WILD-TYPE                                            16
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  EGFR MUTATED                                0
  EGFR WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  EGFR MUTATED                                    1
  EGFR WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  EGFR MUTATED                              0                             2
  EGFR WILD-TYPE                            2                            20
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  EGFR MUTATED                                               0
  EGFR WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  EGFR MUTATED                              0
  EGFR WILD-TYPE                            9
D4V10, multiclass
                                                    clus
vv                                                   EGFR MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           39
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 3
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   EGFR WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            256
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  16
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
D4V12, continuous
                vv
clus              R0  R1  R2  RX
  EGFR MUTATED    42   2   1   3
  EGFR WILD-TYPE 268   9   3  22
D4V13, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  R0           42            268
  R1            2              9
  R2            1              3
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EGFR MUTATED                                  0     3
  EGFR WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED                           3    52
  EGFR WILD-TYPE                        26   325
D4V14, multiclass
                                  clus
vv                                 EGFR MUTATED EGFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              4
  BLACK OR AFRICAN AMERICAN                   3             26
  WHITE                                      52            325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                cls
clus               0   1
  EGFR MUTATED     0  51
  EGFR WILD-TYPE   6 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0   51
  EGFR WILD-TYPE    6  298
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           51            298
[1] 2 2
[1] FALSE

Clustering(5) Variable = STK11 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  STK11 MUTATED    42  30
  STK11 WILD-TYPE 260 125
  STK11 MUTATED STK11 WILD-TYPE 
             72             385 
  STK11 MUTATED STK11 WILD-TYPE 
             30             125 
$`STK11 MUTATED`
TCGA-05-4395 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4432 TCGA-05-5425 
        0.00         2.99        14.96        12.00        25.02        29.00 
TCGA-44-6144 TCGA-44-6776 TCGA-44-6779 TCGA-44-7671 TCGA-44-8120 TCGA-44-A479 
       23.77        63.72        16.44        29.23         8.55        15.98 
TCGA-44-A47F TCGA-49-4486 TCGA-49-4487 TCGA-49-4507 TCGA-50-5072 TCGA-50-5932 
       11.08        76.21        28.11         8.81         8.09        40.60 
TCGA-50-5939 TCGA-53-7813 TCGA-55-6970 TCGA-55-6983 TCGA-55-7574 TCGA-55-8092 
       15.12        13.94        15.25        60.03         3.12         5.06 
TCGA-55-8203 TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 
       17.98        15.42         0.95         0.26         0.49         0.49 
TCGA-55-A492 TCGA-62-A46P TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-64-5774 
       19.59        19.53        54.35        39.25        40.96        87.98 
TCGA-69-7763 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-78-7148 TCGA-78-7152 
       22.68         4.31         1.25        39.09        20.58        39.95 
TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 TCGA-78-7167 
       32.09        64.90        22.92         9.57         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-86-7701 TCGA-86-7713 
       26.53        31.20         8.02        53.33        31.13        38.04 
TCGA-86-8054 TCGA-86-8280 TCGA-86-8359 TCGA-91-6849 TCGA-95-A4VP TCGA-97-8179 
       37.74        23.05        14.60         1.15        19.89        14.30 
TCGA-97-A4M3 TCGA-99-8025 TCGA-99-8032 TCGA-J2-8194 TCGA-MP-A4TD TCGA-MP-A4TE 
       17.75        34.85         1.45        23.80        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-NJ-A4YF TCGA-NJ-A4YP TCGA-NJ-A55O TCGA-NJ-A55R 
       11.05        24.36        71.05         1.64         0.43        19.82 

$`STK11 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        9.01        29.98        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 
       25.02        24.00        15.02        15.02         4.96        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        28.37        28.01        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       27.78        23.15        21.63        23.18        32.45        61.28 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B 
       29.00        13.74        12.66         3.25        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       11.54        13.64        13.45        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       46.72        14.07        32.84        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
       49.28         9.27        14.27        78.67        21.47         8.45 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99         7.59        27.25        34.29        30.54 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        42.51        40.73         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 
        5.49         7.79         2.20        45.34        32.71        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        7.99         0.20         0.13         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
       29.72        15.19         3.29        19.66        19.73         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65         1.08         1.51         2.17        22.16 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        1.45         0.76         0.36        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64        17.62         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R 
       42.38        14.60        88.64        49.25        47.80        56.71 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       67.96        72.30        13.61        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       81.80        38.37         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        4.64        13.87         6.64         6.12        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
       23.38        82.68        26.30        15.35        30.31         9.24 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
       50.33       163.10        27.16         5.69        19.27       129.53 
TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7162 
       21.90       119.51        19.50        38.50         5.88       104.19 
TCGA-78-7163 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
      238.29        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
        5.88        34.39        20.55        32.78        19.89        35.24 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.04        31.20        21.47         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 
        2.60        13.71        12.23        27.68         7.36        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 
       15.65        27.29         2.76        21.40        18.18        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
       20.52        20.84        18.67        20.68        24.56        36.76 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.57        24.30        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TI 
        5.49         5.29        41.59        31.23         2.43        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A 
       19.13        73.91        62.60         0.13        29.13         0.26 
TCGA-O1-A52J 
       59.11 

  STK11 MUTATED STK11 WILD-TYPE 
           0.00            0.07 
  STK11 MUTATED STK11 WILD-TYPE 
          88.14          238.29 
  STK11 MUTATED STK11 WILD-TYPE 
          19.56           19.82 
[1] "0.0 - 88.1 (19.6)"  "0.1 - 238.3 (19.8)"
[1] "hr=" "1.3"
D5V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  STK11 MUTATED         0       19       18         6        13         12
  STK11 WILD-TYPE       4      104      114        41        53         58
                 vv
clus              STAGE IIIB STAGE IV
  STK11 MUTATED            3        5
  STK11 WILD-TYPE          8       20
D5V3, multiclass
            clus
vv           STK11 MUTATED STK11 WILD-TYPE
  STAGE I                0               4
  STAGE IA              19             104
  STAGE IB              18             114
  STAGE IIA              6              41
  STAGE IIB             13              53
  STAGE IIIA            12              58
  STAGE IIIB             3               8
  STAGE IV               5              20
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK11 MUTATED    20  44   7   5
  STK11 WILD-TYPE 135 217  36  13
D5V4, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  T1            20             135
  T2            44             217
  T3             7              36
  T4             5              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
  STK11 MUTATED    47  14    14
  STK11 WILD-TYPE 260  75    58
D5V5, multiclass
       clus
vv      STK11 MUTATED STK11 WILD-TYPE
  N0               47             260
  N1               14              75
  N2+N3            14              58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                 cls
clus                0   1
  STK11 MUTATED    56   5
  STK11 WILD-TYPE 272  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     56    5
  STK11 WILD-TYPE  272   18
   clus
vv  STK11 MUTATED STK11 WILD-TYPE
  0            56             272
  1             5              18
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  STK11 MUTATED    30  46
  STK11 WILD-TYPE 229 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     30   46
  STK11 WILD-TYPE  229  175
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  FEMALE            30             229
  MALE              46             175
[1] 2 2
[1] FALSE
D5V8, binary
                 cls
clus                0   1
  STK11 MUTATED    57   7
  STK11 WILD-TYPE 276  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     57    7
  STK11 WILD-TYPE  276   42
     clus
vv    STK11 MUTATED STK11 WILD-TYPE
  NO             57             276
  YES             7              42
[1] 2 2
[1] FALSE
D5V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STK11 MUTATED                            4                                21
  STK11 WILD-TYPE                         14                                80
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STK11 MUTATED                                                   41
  STK11 WILD-TYPE                                                254
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STK11 MUTATED                                            0
  STK11 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STK11 MUTATED                                               3
  STK11 WILD-TYPE                                            16
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  STK11 MUTATED                                0
  STK11 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  STK11 MUTATED                                    0
  STK11 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STK11 MUTATED                              0                             4
  STK11 WILD-TYPE                            2                            18
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STK11 MUTATED                                               0
  STK11 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  STK11 MUTATED                              3
  STK11 WILD-TYPE                            6
D5V10, multiclass
                                                    clus
vv                                                   STK11 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            41
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  3
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   3
                                                    clus
vv                                                   STK11 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             254
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   16
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   18
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
D5V12, continuous
                 vv
clus               R0  R1  R2  RX
  STK11 MUTATED    51   3   0   3
  STK11 WILD-TYPE 259   8   4  22
D5V13, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  R0            51             259
  R1             3               8
  R2             0               4
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK11 MUTATED                                  0     0
  STK11 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK11 MUTATED                           7    58
  STK11 WILD-TYPE                        22   319
D5V14, multiclass
                                  clus
vv                                 STK11 MUTATED STK11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    7              22
  WHITE                                       58             319
[1] 4 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
  STK11 MUTATED     0  49
  STK11 WILD-TYPE   6 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      0   49
  STK11 WILD-TYPE    6  300
                        clus
vv                       STK11 MUTATED STK11 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            49             300
[1] 2 2
[1] FALSE

Clustering(6) Variable = RBM10 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED    21  11
  RBM10 WILD-TYPE 281 144
  RBM10 MUTATED RBM10 WILD-TYPE 
             32             425 
  RBM10 MUTATED RBM10 WILD-TYPE 
             11             144 
$`RBM10 MUTATED`
TCGA-05-4395 TCGA-05-4403 TCGA-05-4418 TCGA-05-4424 TCGA-44-7659 TCGA-44-7661 
        0.00        19.00         9.01        30.02        22.72        12.03 
TCGA-44-A47A TCGA-49-4494 TCGA-55-6983 TCGA-55-7281 TCGA-55-7727 TCGA-55-7815 
       15.32        35.54        60.03         0.59         1.12         1.78 
TCGA-55-8090 TCGA-55-8205 TCGA-55-8208 TCGA-55-8620 TCGA-55-A490 TCGA-55-A491 
       19.66         1.08        22.16         2.17         1.58        20.58 
TCGA-62-A472 TCGA-64-1676 TCGA-64-5775 TCGA-69-8254 TCGA-73-7498 TCGA-78-7148 
       29.92        56.81         2.04        13.45        39.09        20.58 
TCGA-78-7158 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-91-6828 TCGA-91-6848 
        5.88         8.48        26.53        53.33        10.62         7.36 
TCGA-97-A4M7 TCGA-MP-A4SW 
       20.68        58.45 

$`RBM10 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03        47.05         8.02        20.05         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       14.96        29.98        12.00        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        44.42        38.10        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       23.18        63.72        32.45        61.28        16.44        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F 
       12.66         3.25         8.55        15.98         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       12.66        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 
       24.99        40.54       107.21        70.26         1.74         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.28         1.28         0.79         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
       15.65        17.98         1.51         2.17        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61        16.93        22.65        20.71        21.40 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       39.25        40.96        20.65        81.80        38.37        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K 
        4.41         2.93        12.56        14.01         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       15.35         4.31        30.31         9.24         1.25        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16         5.69        19.27       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 
       39.95       119.51        19.50        38.50        32.09        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 
       22.92         9.57       104.19       238.29        88.14        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        8.02        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       26.47        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       20.52        17.75        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19        38.63         2.76        86.14        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  RBM10 MUTATED RBM10 WILD-TYPE 
           0.00            0.07 
  RBM10 MUTATED RBM10 WILD-TYPE 
          60.03          238.29 
  RBM10 MUTATED RBM10 WILD-TYPE 
          17.16           19.82 
[1] "0.0 - 60.0 (17.2)"  "0.1 - 238.3 (19.8)"
[1] "hr=" "1.3"
D6V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RBM10 MUTATED         0        9        5         1         7          7
  RBM10 WILD-TYPE       4      114      127        46        59         63
                 vv
clus              STAGE IIIB STAGE IV
  RBM10 MUTATED            2        1
  RBM10 WILD-TYPE          9       24
D6V3, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I                0               4
  STAGE IA               9             114
  STAGE IB               5             127
  STAGE IIA              1              46
  STAGE IIB              7              59
  STAGE IIIA             7              63
  STAGE IIIB             2               9
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM10 MUTATED    11  15   4   3
  RBM10 WILD-TYPE 144 246  39  15
D6V4, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  T1            11             144
  T2            15             246
  T3             4              39
  T4             3              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
  RBM10 MUTATED    19   5     8
  RBM10 WILD-TYPE 288  84    64
D6V5, multiclass
       clus
vv      RBM10 MUTATED RBM10 WILD-TYPE
  N0               19             288
  N1                5              84
  N2+N3             8              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                 cls
clus                0   1
  RBM10 MUTATED    24   1
  RBM10 WILD-TYPE 304  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     24    1
  RBM10 WILD-TYPE  304   22
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0            24             304
  1             1              22
[1] 2 2
[1] FALSE
D6V7, binary
                 cls
clus                0   1
  RBM10 MUTATED    10  23
  RBM10 WILD-TYPE 249 198
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     10   23
  RBM10 WILD-TYPE  249  198
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE            10             249
  MALE              23             198
[1] 2 2
[1] FALSE
D6V8, binary
                 cls
clus                0   1
  RBM10 MUTATED    18   4
  RBM10 WILD-TYPE 315  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     18    4
  RBM10 WILD-TYPE  315   45
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO             18             315
  YES             4              45
[1] 2 2
[1] FALSE
D6V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RBM10 MUTATED                            0                                10
  RBM10 WILD-TYPE                         18                                91
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RBM10 MUTATED                                                   21
  RBM10 WILD-TYPE                                                274
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RBM10 MUTATED                                            0
  RBM10 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RBM10 MUTATED                                               1
  RBM10 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  RBM10 MUTATED                                0
  RBM10 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  RBM10 MUTATED                                    0
  RBM10 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RBM10 MUTATED                              0                             0
  RBM10 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RBM10 MUTATED                                               0
  RBM10 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  RBM10 MUTATED                              1
  RBM10 WILD-TYPE                            8
D6V10, multiclass
                                                    clus
vv                                                   RBM10 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            21
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   RBM10 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               91
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             274
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
D6V12, continuous
                 vv
clus               R0  R1  R2  RX
  RBM10 MUTATED    27   2   0   0
  RBM10 WILD-TYPE 283   9   4  25
D6V13, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0            27             283
  R1             2               9
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM10 MUTATED                                  0     0
  RBM10 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED                           0    26
  RBM10 WILD-TYPE                        29   351
D6V14, multiclass
                                  clus
vv                                 RBM10 MUTATED RBM10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       26             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                 cls
clus                0   1
  RBM10 MUTATED     0  20
  RBM10 WILD-TYPE   6 329
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      0   20
  RBM10 WILD-TYPE    6  329
                        clus
vv                       RBM10 MUTATED RBM10 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            20             329
[1] 2 2
[1] FALSE

Clustering(7) Variable = RB1 MUTATION ANALYSIS
D7V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    18   7
  RB1 WILD-TYPE 284 148
  RB1 MUTATED RB1 WILD-TYPE 
           25           432 
  RB1 MUTATED RB1 WILD-TYPE 
            7           148 
$`RB1 MUTATED`
TCGA-05-4397 TCGA-05-4415 TCGA-35-5375 TCGA-44-6775 TCGA-44-7660 TCGA-44-7669 
       24.03         2.99         8.68        23.18        19.46        18.87 
TCGA-55-6968 TCGA-55-8208 TCGA-55-A48Z TCGA-78-7143 TCGA-86-8056 TCGA-86-8074 
       42.51        22.16        21.40       163.10         4.57         0.79 
TCGA-86-8358 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6847 TCGA-93-A4JN 
       21.47        10.62        41.36         2.60        27.68        23.61 
TCGA-93-A4JP TCGA-95-7562 TCGA-95-7947 TCGA-97-7553 TCGA-97-8172 TCGA-J2-A4AE 
       19.00         2.86        15.68        43.79        17.92        35.47 
TCGA-L4-A4E5 
       19.00 

$`RB1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
       12.03         7.17        36.07        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.33        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94        35.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
        0.07        32.65         0.79        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
       15.65        17.98         1.08         1.51         2.17        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       39.09        50.33        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 
       19.89        35.24        37.74         4.08        24.33        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        31.20        23.05        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6831 
       29.46        24.23        13.64        26.47         1.97        10.19 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       13.71        12.23         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
        6.12         1.08        17.29        41.82        16.54        18.67 
TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 
       19.89        31.69        64.60        63.52        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       23.80        18.08        32.48        14.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  RB1 MUTATED RB1 WILD-TYPE 
         0.79          0.00 
  RB1 MUTATED RB1 WILD-TYPE 
       163.10        238.29 
  RB1 MUTATED RB1 WILD-TYPE 
        19.46         19.82 
[1] "0.8 - 163.1 (19.5)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.2"
D7V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RB1 MUTATED         1        6        8         3         1          2
  RB1 WILD-TYPE       3      117      124        44        65         68
               vv
clus            STAGE IIIB STAGE IV
  RB1 MUTATED            2        3
  RB1 WILD-TYPE          9       22
D7V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I              1             3
  STAGE IA             6           117
  STAGE IB             8           124
  STAGE IIA            3            44
  STAGE IIB            1            65
  STAGE IIIA           2            68
  STAGE IIIB           2             9
  STAGE IV             3            22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  RB1 MUTATED    11  12   0   2
  RB1 WILD-TYPE 144 249  43  16
D7V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1          11           144
  T2          12           249
  T3           0            43
  T4           2            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
  RB1 MUTATED    18   4     3
  RB1 WILD-TYPE 289  85    69
D7V5, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  N0             18           289
  N1              4            85
  N2+N3           3            69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
               cls
clus              0   1
  RB1 MUTATED    15   3
  RB1 WILD-TYPE 313  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     15    3
  RB1 WILD-TYPE  313   20
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          15           313
  1           3            20
[1] 2 2
[1] FALSE
D7V7, binary
               cls
clus              0   1
  RB1 MUTATED    13  13
  RB1 WILD-TYPE 246 208
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     13   13
  RB1 WILD-TYPE  246  208
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          13           246
  MALE            13           208
[1] 2 2
[1] FALSE
D7V8, binary
               cls
clus              0   1
  RB1 MUTATED    18   3
  RB1 WILD-TYPE 315  46
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     18    3
  RB1 WILD-TYPE  315   46
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           18           315
  YES           3            46
[1] 2 2
[1] FALSE
D7V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RB1 MUTATED                            2                                 5
  RB1 WILD-TYPE                         16                                96
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RB1 MUTATED                                                   15
  RB1 WILD-TYPE                                                280
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RB1 MUTATED                                            0
  RB1 WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RB1 MUTATED                                               3
  RB1 WILD-TYPE                                            16
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  RB1 MUTATED                                0
  RB1 WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  RB1 MUTATED                                    0                            0
  RB1 WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  RB1 MUTATED                               1
  RB1 WILD-TYPE                            21
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RB1 MUTATED                                               0
  RB1 WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  RB1 MUTATED                              0
  RB1 WILD-TYPE                            9
D7V10, multiclass
                                                    clus
vv                                                   RB1 MUTATED RB1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   2            16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            5            96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          15           280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                3            16
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                1            21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
D7V12, continuous
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED    16   0   0   4
  RB1 WILD-TYPE 294  11   4  21
D7V13, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          16           294
  R1           0            11
  R2           0             4
  RX           4            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     1
  RB1 WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           2    20
  RB1 WILD-TYPE                        27   357
D7V14, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  2            27
  WHITE                                     20           357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, binary
               cls
clus              0   1
  RB1 MUTATED     1  21
  RB1 WILD-TYPE   5 328
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1   21
  RB1 WILD-TYPE    5  328
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          21           328
[1] 2 2
[1] FALSE

Clustering(8) Variable = ARID1A MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    20   9
  ARID1A WILD-TYPE 282 146
  ARID1A MUTATED ARID1A WILD-TYPE 
              29              428 
  ARID1A MUTATED ARID1A WILD-TYPE 
               9              146 
$`ARID1A MUTATED`
TCGA-05-4382 TCGA-05-4425 TCGA-05-4427 TCGA-05-5715 TCGA-38-4631 TCGA-44-6147 
       19.96        21.99        26.01         2.04        11.64        27.78 
TCGA-44-7667 TCGA-44-7670 TCGA-55-5899 TCGA-55-7725 TCGA-55-7815 TCGA-55-7914 
       36.07        29.00         2.86         1.28         1.78         6.15 
TCGA-55-8089 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-A490 TCGA-64-1681 
        3.29        15.65        22.16        15.42         1.58        38.37 
TCGA-67-3771 TCGA-78-7156 TCGA-78-7167 TCGA-86-8278 TCGA-91-6831 TCGA-97-7938 
       20.05        32.09        88.14        31.04        10.19         0.59 
TCGA-99-8025 TCGA-L4-A4E5 TCGA-MN-A4N4 TCGA-MP-A4TC TCGA-MP-A4TI 
       34.85        19.00        38.63         2.43        14.10 

$`ARID1A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 
        4.96        29.00        22.03         9.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       35.28        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       44.42        38.10        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
       19.56         9.93        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
        7.17        18.87        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       35.21        23.05        48.62         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 
       23.18         1.28         1.12         0.79         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 
       17.98         1.08         1.51         2.17         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       81.80        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       28.47        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
      119.51        19.50        38.50         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29         8.48        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
       24.33         0.79        22.82        32.65        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62        41.36         1.97         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
       64.60        63.52        43.79        25.48         5.95         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       35.47        32.48        14.30         6.35        10.09        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD 
       58.85         5.49         5.29        41.59        31.23        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        11.05        24.36        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.59             0.00 
  ARID1A MUTATED ARID1A WILD-TYPE 
           88.14           238.29 
  ARID1A MUTATED ARID1A WILD-TYPE 
           19.00            19.82 
[1] "0.6 - 88.1 (19.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.2"
D8V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARID1A MUTATED         1       11        5         4         3          3
  ARID1A WILD-TYPE       3      112      127        43        63         67
                  vv
clus               STAGE IIIB STAGE IV
  ARID1A MUTATED            0        3
  ARID1A WILD-TYPE         11       22
D8V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 1                3
  STAGE IA               11              112
  STAGE IB                5              127
  STAGE IIA               4               43
  STAGE IIB               3               63
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                3               22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1A MUTATED    15  12   2   1
  ARID1A WILD-TYPE 140 249  41  17
D8V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1             15              140
  T2             12              249
  T3              2               41
  T4              1               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
  ARID1A MUTATED    19   7     3
  ARID1A WILD-TYPE 288  82    69
D8V5, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  N0                19              288
  N1                 7               82
  N2+N3              3               69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    18   3
  ARID1A WILD-TYPE 310  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     18    3
  ARID1A WILD-TYPE  310   20
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             18              310
  1              3               20
[1] 2 2
[1] FALSE
D8V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED    18  12
  ARID1A WILD-TYPE 241 209
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     18   12
  ARID1A WILD-TYPE  241  209
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             18              241
  MALE               12              209
[1] 2 2
[1] FALSE
D8V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    20   0
  ARID1A WILD-TYPE 313  49
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     20    0
  ARID1A WILD-TYPE  313   49
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              20              313
  YES              0               49
[1] 2 2
[1] FALSE
D8V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARID1A MUTATED                            0                                 5
  ARID1A WILD-TYPE                         18                                96
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                   23
  ARID1A WILD-TYPE                                                272
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARID1A MUTATED                                            0
  ARID1A WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARID1A MUTATED                                               1
  ARID1A WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ARID1A MUTATED                                0
  ARID1A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ARID1A MUTATED                                    0
  ARID1A WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ARID1A MUTATED                              0                             1
  ARID1A WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARID1A MUTATED                                               0
  ARID1A WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ARID1A MUTATED                              0
  ARID1A WILD-TYPE                            9
D8V10, multiclass
                                                    clus
vv                                                   ARID1A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             23
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ARID1A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              272
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
D8V12, continuous
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    25   1   0   0
  ARID1A WILD-TYPE 285  10   4  25
D8V13, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             25              285
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  0     0
  ARID1A WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           2    22
  ARID1A WILD-TYPE                        27   355
D8V14, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                        22              355
[1] 4 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
  ARID1A MUTATED     1  21
  ARID1A WILD-TYPE   5 328
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   21
  ARID1A WILD-TYPE    5  328
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             21              328
[1] 2 2
[1] FALSE

Clustering(9) Variable = NF1 MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    36  17
  NF1 WILD-TYPE 266 138
  NF1 MUTATED NF1 WILD-TYPE 
           53           404 
  NF1 MUTATED NF1 WILD-TYPE 
           17           138 
$`NF1 MUTATED`
TCGA-05-4424 TCGA-38-4629 TCGA-38-4631 TCGA-44-2656 TCGA-44-2657 TCGA-44-3918 
       30.02        28.41        11.64        46.98        44.42        34.06 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6775 TCGA-44-7667 TCGA-44-8119 TCGA-49-4488 
       28.37        23.77        23.18        36.07         3.25        28.57 
TCGA-49-6767 TCGA-50-5045 TCGA-50-5068 TCGA-50-5072 TCGA-50-5946 TCGA-50-6593 
       22.26        71.47        49.28         8.09        22.55        11.05 
TCGA-50-8457 TCGA-55-1592 TCGA-55-6971 TCGA-55-6975 TCGA-55-7724 TCGA-55-7907 
       36.99        23.05         0.82         3.88        23.18         0.53 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-8205 TCGA-55-8621 TCGA-55-A4DG 
       19.82         0.16         3.29         1.08        16.93        19.99 
TCGA-62-A46S TCGA-64-1679 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 
       54.35        81.80        13.61         5.42         4.41         2.93 
TCGA-73-4658 TCGA-73-4676 TCGA-78-7146 TCGA-78-7535 TCGA-78-7542 TCGA-86-8073 
       52.60         9.24         5.69        31.20        10.55        24.33 
TCGA-86-8279 TCGA-86-8669 TCGA-91-6829 TCGA-95-7043 TCGA-95-7944 TCGA-97-7547 
       31.20        30.84        41.36        16.54        12.39        64.60 
TCGA-97-7553 TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MP-A4SY TCGA-NJ-A55A 
       43.79        19.00        10.09        49.35         0.26 

$`NF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       37.71        49.05        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
        4.37        38.10        42.77        37.15        38.24        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       26.56        33.30        28.01        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 
       22.72        19.46        12.03         7.17        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       29.23        13.74        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.11        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 
       55.33        17.16        11.64        20.52        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       60.16        31.04         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
       42.35         3.91        25.55        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
        0.72        10.13         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94        35.21        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6978 
        0.79        42.51        40.73        15.25        48.49         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
        7.99         0.20         0.13         3.12         1.32         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.48        17.65         6.15        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.61         2.17        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 
       20.58        19.59         0.92        15.81        20.19         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        56.81        20.65        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 
        6.64         6.12        22.68         7.56         6.05        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        17.16         2.01         6.90 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
        1.25        39.09        50.33       163.10        27.16        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
      104.19       238.29         8.48        88.14        26.53         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
       35.24        37.74         4.08         4.57         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
       24.23        13.64        26.47        10.62         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
       17.29        41.82         2.86        18.67        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 
       35.47        32.48        14.30         6.35        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        86.14        58.45        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O 
       71.05        62.60         0.13         1.64        29.13         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  NF1 MUTATED NF1 WILD-TYPE 
         0.16          0.00 
  NF1 MUTATED NF1 WILD-TYPE 
        81.80        238.29 
  NF1 MUTATED NF1 WILD-TYPE 
       22.550        19.625 
[1] "0.2 - 81.8 (22.6)"  "0.0 - 238.3 (19.6)"
[1] "hr=" "1.1"
D9V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NF1 MUTATED         1       17       18         3        11          4
  NF1 WILD-TYPE       3      106      114        44        55         66
               vv
clus            STAGE IIIB STAGE IV
  NF1 MUTATED            0        1
  NF1 WILD-TYPE         11       24
D9V3, multiclass
            clus
vv           NF1 MUTATED NF1 WILD-TYPE
  STAGE I              1             3
  STAGE IA            17           106
  STAGE IB            18           114
  STAGE IIA            3            44
  STAGE IIB           11            55
  STAGE IIIA           4            66
  STAGE IIIB           0            11
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NF1 MUTATED    18  30   6   1
  NF1 WILD-TYPE 137 231  37  17
D9V4, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1          18           137
  T2          30           231
  T3           6            37
  T4           1            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
  NF1 MUTATED    42   8     4
  NF1 WILD-TYPE 265  81    68
D9V5, multiclass
       clus
vv      NF1 MUTATED NF1 WILD-TYPE
  N0             42           265
  N1              8            81
  N2+N3           4            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
               cls
clus              0   1
  NF1 MUTATED    33   0
  NF1 WILD-TYPE 295  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     33    0
  NF1 WILD-TYPE  295   23
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0          33           295
  1           0            23
[1] 2 2
[1] FALSE
D9V7, binary
               cls
clus              0   1
  NF1 MUTATED    29  26
  NF1 WILD-TYPE 230 195
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     29   26
  NF1 WILD-TYPE  230  195
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          29           230
  MALE            26           195
[1] 2 2
[1] FALSE
D9V8, binary
               cls
clus              0   1
  NF1 MUTATED    39   5
  NF1 WILD-TYPE 294  44
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     39    5
  NF1 WILD-TYPE  294   44
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           39           294
  YES           5            44
[1] 2 2
[1] FALSE
D9V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NF1 MUTATED                            1                                10
  NF1 WILD-TYPE                         17                                91
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NF1 MUTATED                                                   39
  NF1 WILD-TYPE                                                256
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NF1 MUTATED                                            0
  NF1 WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NF1 MUTATED                                               3
  NF1 WILD-TYPE                                            16
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  NF1 MUTATED                                0
  NF1 WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  NF1 MUTATED                                    0                            0
  NF1 WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  NF1 MUTATED                               2
  NF1 WILD-TYPE                            20
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NF1 MUTATED                                               0
  NF1 WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  NF1 MUTATED                              0
  NF1 WILD-TYPE                            9
D9V10, multiclass
                                                    clus
vv                                                   NF1 MUTATED NF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           10            91
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          39           256
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                3            16
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                2            20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
D9V12, continuous
               vv
clus             R0  R1  R2  RX
  NF1 MUTATED    34   1   0   2
  NF1 WILD-TYPE 276  10   4  23
D9V13, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0          34           276
  R1           1            10
  R2           0             4
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  0     0
  NF1 WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           3    50
  NF1 WILD-TYPE                        26   327
D9V14, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  3            26
  WHITE                                     50           327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
               cls
clus              0   1
  NF1 MUTATED     1  46
  NF1 WILD-TYPE   5 303
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1   46
  NF1 WILD-TYPE    5  303
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          46           303
[1] 2 2
[1] FALSE

Clustering(10) Variable = SMARCA4 MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED    22  14
  SMARCA4 WILD-TYPE 280 141
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               36               421 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               14               141 
$`SMARCA4 MUTATED`
TCGA-05-4432 TCGA-05-5420 TCGA-35-5375 TCGA-38-4631 TCGA-44-2656 TCGA-44-8117 
       25.02        15.02         8.68        11.64        46.98        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-49-6742 TCGA-49-6767 TCGA-50-5072 TCGA-50-5930 
        3.25        15.98        16.04        22.26         8.09         9.27 
TCGA-50-5936 TCGA-53-7624 TCGA-55-6543 TCGA-55-6969 TCGA-55-6975 TCGA-55-8089 
        8.45        34.29         0.07        40.73         3.88         3.29 
TCGA-55-A48Y TCGA-55-A48Z TCGA-62-A46O TCGA-67-3771 TCGA-69-7980 TCGA-69-8255 
       20.71        21.40        47.80        20.05        12.56         4.24 
TCGA-78-7148 TCGA-78-8640 TCGA-78-8660 TCGA-86-7711 TCGA-86-8585 TCGA-86-8674 
       20.58       232.18        10.55        34.39         1.15        26.50 
TCGA-97-8175 TCGA-97-8176 TCGA-J2-A4AD TCGA-MP-A4SY TCGA-MP-A4TA TCGA-NJ-A4YQ 
       18.12        15.39        18.08        49.35        31.23        29.13 

$`SMARCA4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        44.61        14.73        26.30         4.37 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       44.42        38.10        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
       13.74         8.55        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        53.29        55.33        17.16        11.64 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 
       49.28        14.27        40.60        78.67        21.47        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        36.99         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
       35.21        23.05        48.62         2.86        32.65         0.79 
TCGA-55-6968 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 
       42.51        15.25         0.82        48.49         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       16.93        22.65         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        88.64        49.25        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
        2.93        14.01        13.45        17.16         2.01         6.90 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        82.68        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        19.27       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 
       10.55        50.24        39.75        77.59       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        31.13        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       21.47        14.60        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       28.34        29.46        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       18.67        17.92         5.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45        21.57        24.30        23.80        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        86.14        58.45        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        41.59         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
             0.07              0.00 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           232.18            238.29 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
            17.06             19.82 
[1] "0.1 - 232.2 (17.1)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.4"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SMARCA4 MUTATED         1        8        9         5         7          6
  SMARCA4 WILD-TYPE       3      115      123        42        59         64
                   vv
clus                STAGE IIIB STAGE IV
  SMARCA4 MUTATED            1        1
  SMARCA4 WILD-TYPE         10       24
D10V3, multiclass
            clus
vv           SMARCA4 MUTATED SMARCA4 WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 8               115
  STAGE IB                 9               123
  STAGE IIA                5                42
  STAGE IIB                7                59
  STAGE IIIA               6                64
  STAGE IIIB               1                10
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCA4 MUTATED    11  24   3   0
  SMARCA4 WILD-TYPE 144 237  40  18
D10V4, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  T1              11               144
  T2              24               237
  T3               3                40
  T4               0                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
  SMARCA4 MUTATED    21  10     6
  SMARCA4 WILD-TYPE 286  79    66
D10V5, multiclass
       clus
vv      SMARCA4 MUTATED SMARCA4 WILD-TYPE
  N0                 21               286
  N1                 10                79
  N2+N3               6                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    32   1
  SMARCA4 WILD-TYPE 296  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     32    1
  SMARCA4 WILD-TYPE  296   22
   clus
vv  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  0              32               296
  1               1                22
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    14  24
  SMARCA4 WILD-TYPE 245 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     14   24
  SMARCA4 WILD-TYPE  245  197
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE              14               245
  MALE                24               197
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    23   4
  SMARCA4 WILD-TYPE 310  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     23    4
  SMARCA4 WILD-TYPE  310   45
     clus
vv    SMARCA4 MUTATED SMARCA4 WILD-TYPE
  NO               23               310
  YES               4                45
[1] 2 2
[1] FALSE
D10V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SMARCA4 MUTATED                            1
  SMARCA4 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SMARCA4 MUTATED                                   5
  SMARCA4 WILD-TYPE                                96
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SMARCA4 MUTATED                                                   24
  SMARCA4 WILD-TYPE                                                271
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SMARCA4 MUTATED                                            1
  SMARCA4 WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SMARCA4 MUTATED                                               0
  SMARCA4 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  SMARCA4 MUTATED                                0
  SMARCA4 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  SMARCA4 MUTATED                                    0
  SMARCA4 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SMARCA4 MUTATED                              0                             1
  SMARCA4 WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SMARCA4 MUTATED                                               4
  SMARCA4 WILD-TYPE                                             1
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  SMARCA4 MUTATED                              2
  SMARCA4 WILD-TYPE                            7
D10V10, multiclass
                                                    clus
vv                                                   SMARCA4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              24
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   SMARCA4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               271
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      1
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
D10V12, continuous
                   vv
clus                 R0  R1  R2  RX
  SMARCA4 MUTATED    23   0   0   2
  SMARCA4 WILD-TYPE 287  11   4  23
D10V13, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  R0              23               287
  R1               0                11
  R2               0                 4
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCA4 MUTATED                                  0     0
  SMARCA4 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCA4 MUTATED                           2    31
  SMARCA4 WILD-TYPE                        27   346
D10V14, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         31               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     3  26
  SMARCA4 WILD-TYPE   3 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      3   26
  SMARCA4 WILD-TYPE    3  323
                        clus
vv                       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  NOT HISPANIC OR LATINO              26               323
[1] 2 2
[1] FALSE

Clustering(11) Variable = BRAF MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  BRAF MUTATED    24  11
  BRAF WILD-TYPE 278 144
  BRAF MUTATED BRAF WILD-TYPE 
            35            422 
  BRAF MUTATED BRAF WILD-TYPE 
            11            144 
$`BRAF MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-5428 TCGA-44-2656 TCGA-44-3918 
       50.07        19.96        45.01        22.03        46.98        34.06 
TCGA-44-6774 TCGA-50-5044 TCGA-50-5930 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
       21.63        20.52         9.27         9.37        29.03        22.55 
TCGA-50-6594 TCGA-53-A4EZ TCGA-55-6968 TCGA-55-6979 TCGA-55-7903 TCGA-55-8092 
       12.16        35.21        42.51         7.79        18.64         5.06 
TCGA-55-8506 TCGA-55-8511 TCGA-62-A46V TCGA-62-A472 TCGA-69-7765 TCGA-78-7153 
        0.36         0.30        72.30        29.92         5.42       119.51 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8660 TCGA-78-8662 TCGA-86-7714 
       53.33        26.01        50.24        10.55       110.50        20.55 
TCGA-91-A4BD TCGA-95-7039 TCGA-97-A4M7 TCGA-L4-A4E6 TCGA-MN-A4N1 
       19.82        41.82        20.68        14.30        27.19 

$`BRAF WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
        3.98        14.01        37.02         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       47.05         8.02        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
        4.96        29.00         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
       44.42        38.10        42.77        37.15        38.24        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
        9.93        27.78        23.15        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        11.64        22.26        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         8.09        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-6590 
       78.67        21.47         8.45        15.12        25.12        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        25.55        11.05         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        5.49         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
       29.72        15.19         3.29        19.66        19.73         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
        0.49        17.72         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 
       54.35        67.96        13.61        39.25        40.96        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         7.56         6.05         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        6.90        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 
       88.14        26.53        31.20         8.02        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
      232.18        39.75        77.59        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        38.04        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       26.50        29.46        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.18         1.45        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       19.00         6.35        10.09        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  BRAF MUTATED BRAF WILD-TYPE 
           0.3            0.0 
  BRAF MUTATED BRAF WILD-TYPE 
        119.51         238.29 
  BRAF MUTATED BRAF WILD-TYPE 
        22.030         19.515 
[1] "0.3 - 119.5 (22.0)" "0.0 - 238.3 (19.5)"
[1] "hr=" "1.4"
D11V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  BRAF MUTATED         0        7       11         5         7          5
  BRAF WILD-TYPE       4      116      121        42        59         65
                vv
clus             STAGE IIIB STAGE IV
  BRAF MUTATED            1        2
  BRAF WILD-TYPE         10       23
D11V3, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I               0              4
  STAGE IA              7            116
  STAGE IB             11            121
  STAGE IIA             5             42
  STAGE IIB             7             59
  STAGE IIIA            5             65
  STAGE IIIB            1             10
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRAF MUTATED    12  19   5   2
  BRAF WILD-TYPE 143 242  38  16
D11V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1           12            143
  T2           19            242
  T3            5             38
  T4            2             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
  BRAF MUTATED    25   8     5
  BRAF WILD-TYPE 282  81    67
D11V5, multiclass
       clus
vv      BRAF MUTATED BRAF WILD-TYPE
  N0              25            282
  N1               8             81
  N2+N3            5             67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                cls
clus               0   1
  BRAF MUTATED    28   1
  BRAF WILD-TYPE 300  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     28    1
  BRAF WILD-TYPE  300   22
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0           28            300
  1            1             22
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus               0   1
  BRAF MUTATED    16  22
  BRAF WILD-TYPE 243 199
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     16   22
  BRAF WILD-TYPE  243  199
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           16            243
  MALE             22            199
[1] 2 2
[1] FALSE
D11V8, binary
                cls
clus               0   1
  BRAF MUTATED    24   8
  BRAF WILD-TYPE 309  41
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     24    8
  BRAF WILD-TYPE  309   41
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            24            309
  YES            8             41
[1] 2 2
[1] FALSE
D11V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  BRAF MUTATED                            1                                14
  BRAF WILD-TYPE                         17                                87
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  BRAF MUTATED                                                   23
  BRAF WILD-TYPE                                                272
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  BRAF MUTATED                                            0
  BRAF WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  BRAF MUTATED                                               0
  BRAF WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  BRAF MUTATED                                0
  BRAF WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  BRAF MUTATED                                    0
  BRAF WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  BRAF MUTATED                              0                             0
  BRAF WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  BRAF MUTATED                                               0
  BRAF WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  BRAF MUTATED                              0
  BRAF WILD-TYPE                            9
D11V10, multiclass
                                                    clus
vv                                                   BRAF MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            14
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           23
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   BRAF WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            272
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
D11V12, continuous
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED    24   0   0   3
  BRAF WILD-TYPE 286  11   4  22
D11V13, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           24            286
  R1            0             11
  R2            0              4
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRAF MUTATED                                  0     0
  BRAF WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED                           4    24
  BRAF WILD-TYPE                        25   353
D11V14, multiclass
                                  clus
vv                                 BRAF MUTATED BRAF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   4             25
  WHITE                                      24            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, binary
                cls
clus               0   1
  BRAF MUTATED     1  21
  BRAF WILD-TYPE   5 328
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1   21
  BRAF WILD-TYPE    5  328
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           21            328
[1] 2 2
[1] FALSE

Clustering(12) Variable = MGA MUTATION ANALYSIS
D12V1, survival
               sevent
clus2             0   1
  MGA MUTATED    28  12
  MGA WILD-TYPE 274 143
  MGA MUTATED MGA WILD-TYPE 
           40           417 
  MGA MUTATED MGA WILD-TYPE 
           12           143 
$`MGA MUTATED`
TCGA-05-4405 TCGA-05-4418 TCGA-05-5428 TCGA-05-5715 TCGA-35-5375 TCGA-38-4628 
       20.05         9.01        22.03         2.04         8.68        49.05 
TCGA-44-5644 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-A4SU TCGA-49-4494 
       28.37        29.00        29.23        12.66        13.45        35.54 
TCGA-49-6743 TCGA-49-6745 TCGA-50-5931 TCGA-55-6712 TCGA-55-6968 TCGA-55-7574 
       53.29        17.16        14.27         0.79        42.51         3.12 
TCGA-55-7907 TCGA-55-8208 TCGA-55-8506 TCGA-55-8511 TCGA-55-A490 TCGA-64-5779 
        0.53        22.16         0.36         0.30         1.58        28.41 
TCGA-69-7763 TCGA-69-7974 TCGA-69-A59K TCGA-71-8520 TCGA-73-4668 TCGA-78-7156 
       22.68         6.05        17.16         6.90        15.35        32.09 
TCGA-78-7220 TCGA-86-7955 TCGA-91-6829 TCGA-91-A4BD TCGA-93-A4JQ TCGA-95-7039 
       26.53        35.24        41.36        19.82        17.29        41.82 
TCGA-95-7043 TCGA-97-A4LX TCGA-L9-A443 TCGA-L9-A444 
       16.54        20.19         6.35        10.09 

$`MGA WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 
       15.02         4.96        29.00         9.04         7.40         5.98 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       97.74       120.79        37.71        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        13.74         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       15.32         9.44        11.08        11.54        13.64        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
        8.81        29.46        29.75        55.89        16.04        55.33 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
       60.16        31.04        49.28         8.09         9.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
       23.05        48.62         2.86         0.07        32.65        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.20         0.13         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 
        1.12         0.79         1.78         1.45        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
       15.65        17.98         1.08         1.51         2.17        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
       81.80        38.37        87.98         2.04        42.90        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        4.64        13.87         6.64         6.12        13.61         5.42 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        4.24         2.01        52.60        23.38        82.68        26.30 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
       21.90        39.95       119.51        19.50        38.50         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       38.04        20.55        32.78        19.89        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
       24.23        13.64        26.47        10.62         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7347 
       16.18        16.60        14.27         1.18         1.45        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7562 
       17.46         6.12        23.61         1.08        19.00         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       21.60        20.58        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       32.48        19.00        14.30        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  MGA MUTATED MGA WILD-TYPE 
          0.3           0.0 
  MGA MUTATED MGA WILD-TYPE 
        53.29        238.29 
  MGA MUTATED MGA WILD-TYPE 
       17.225        19.820 
[1] "0.3 - 53.3 (17.2)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.2"
D12V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MGA MUTATED         0        7       12         6         5          8
  MGA WILD-TYPE       4      116      120        41        61         62
               vv
clus            STAGE IIIB STAGE IV
  MGA MUTATED            0        2
  MGA WILD-TYPE         11       23
D12V3, multiclass
            clus
vv           MGA MUTATED MGA WILD-TYPE
  STAGE I              0             4
  STAGE IA             7           116
  STAGE IB            12           120
  STAGE IIA            6            41
  STAGE IIB            5            61
  STAGE IIIA           8            62
  STAGE IIIB           0            11
  STAGE IV             2            23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MGA MUTATED    12  22   5   1
  MGA WILD-TYPE 143 239  38  17
D12V4, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  T1          12           143
  T2          22           239
  T3           5            38
  T4           1            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
  MGA MUTATED    24   8     8
  MGA WILD-TYPE 283  81    64
D12V5, multiclass
       clus
vv      MGA MUTATED MGA WILD-TYPE
  N0             24           283
  N1              8            81
  N2+N3           8            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
               cls
clus              0   1
  MGA MUTATED    22   2
  MGA WILD-TYPE 306  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     22    2
  MGA WILD-TYPE  306   21
   clus
vv  MGA MUTATED MGA WILD-TYPE
  0          22           306
  1           2            21
[1] 2 2
[1] FALSE
D12V7, binary
               cls
clus              0   1
  MGA MUTATED    22  18
  MGA WILD-TYPE 237 203
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     22   18
  MGA WILD-TYPE  237  203
        clus
vv       MGA MUTATED MGA WILD-TYPE
  FEMALE          22           237
  MALE            18           203
[1] 2 2
[1] FALSE
D12V8, binary
               cls
clus              0   1
  MGA MUTATED    24   7
  MGA WILD-TYPE 309  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     24    7
  MGA WILD-TYPE  309   42
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO           24           309
  YES           7            42
[1] 2 2
[1] FALSE
D12V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MGA MUTATED                            2                                12
  MGA WILD-TYPE                         16                                89
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MGA MUTATED                                                   23
  MGA WILD-TYPE                                                272
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MGA MUTATED                                            0
  MGA WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MGA MUTATED                                               1
  MGA WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  MGA MUTATED                                1
  MGA WILD-TYPE                              1
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  MGA MUTATED                                    1                            0
  MGA WILD-TYPE                                  2                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  MGA MUTATED                               0
  MGA WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MGA MUTATED                                               0
  MGA WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  MGA MUTATED                              0
  MGA WILD-TYPE                            9
D12V10, multiclass
                                                    clus
vv                                                   MGA MUTATED MGA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   2            16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           12            89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          23           272
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           1             2
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
D12V12, continuous
               vv
clus             R0  R1  R2  RX
  MGA MUTATED    22   1   0   3
  MGA WILD-TYPE 288  10   4  22
D12V13, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          22           288
  R1           1            10
  R2           0             4
  RX           3            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGA MUTATED                                  1     1
  MGA WILD-TYPE                                0     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MGA MUTATED                           2    32
  MGA WILD-TYPE                        27   345
D12V14, multiclass
                                  clus
vv                                 MGA MUTATED MGA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  2            27
  WHITE                                     32           345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
               cls
clus              0   1
  MGA MUTATED     1  30
  MGA WILD-TYPE   5 319
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED      1   30
  MGA WILD-TYPE    5  319
                        clus
vv                       MGA MUTATED MGA WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          30           319
[1] 2 2
[1] FALSE

Clustering(13) Variable = FTSJD1 MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2                0   1
  FTSJD1 MUTATED    17   7
  FTSJD1 WILD-TYPE 285 148
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
              24              433 
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
               7              148 
$`FTSJD1 MUTATED`
TCGA-05-4420 TCGA-38-4625 TCGA-44-3398 TCGA-44-4112 TCGA-50-5930 TCGA-50-8457 
       29.98        97.74        38.24        26.56         9.27        36.99 
TCGA-55-8206 TCGA-55-8506 TCGA-55-8511 TCGA-55-8514 TCGA-55-A490 TCGA-55-A491 
        1.51         0.36         0.30         6.64         1.58        20.58 
TCGA-64-1679 TCGA-73-4658 TCGA-78-7155 TCGA-78-8662 TCGA-86-A4JF TCGA-93-8067 
       81.80        52.60        38.50       110.50        24.23         6.12 
TCGA-95-A4VN TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-MP-A4SV TCGA-MP-A4TH TCGA-NJ-A4YP 
       18.18        32.48        19.00        86.14        24.36         1.64 

$`FTSJD1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         5.98         8.68       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       37.15        34.06        33.73        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.23        13.74        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.09        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12         9.37        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       41.69         0.72        10.13         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94        35.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65        17.98         1.08         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.26         0.49 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       17.72         0.10         4.80        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 
       39.25        40.96        29.92        56.81        20.65        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        17.16         2.01         6.90        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        50.33       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
      232.18        39.75        77.59        10.55        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        28.34        26.50        29.46        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
        2.76        21.40        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       35.47        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        11.05        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
             0.3              0.0 
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
          110.50           238.29 
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
          24.295           19.730 
[1] "0.3 - 110.5 (24.3)" "0.0 - 238.3 (19.7)"
[1] "hr=" "1.6"
D13V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FTSJD1 MUTATED         1        6       11         2         2          2
  FTSJD1 WILD-TYPE       3      117      121        45        64         68
                  vv
clus               STAGE IIIB STAGE IV
  FTSJD1 MUTATED            0        0
  FTSJD1 WILD-TYPE         11       25
D13V3, multiclass
            clus
vv           FTSJD1 MUTATED FTSJD1 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                6              117
  STAGE IB               11              121
  STAGE IIA               2               45
  STAGE IIB               2               64
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FTSJD1 MUTATED     8  14   2   0
  FTSJD1 WILD-TYPE 147 247  41  18
D13V4, multiclass
    clus
vv   FTSJD1 MUTATED FTSJD1 WILD-TYPE
  T1              8              147
  T2             14              247
  T3              2               41
  T4              0               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
  FTSJD1 MUTATED    21   1     2
  FTSJD1 WILD-TYPE 286  88    70
D13V5, multiclass
       clus
vv      FTSJD1 MUTATED FTSJD1 WILD-TYPE
  N0                21              286
  N1                 1               88
  N2+N3              2               70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                  cls
clus                 0   1
  FTSJD1 MUTATED    17   0
  FTSJD1 WILD-TYPE 311  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FTSJD1 MUTATED     17    0
  FTSJD1 WILD-TYPE  311   23
   clus
vv  FTSJD1 MUTATED FTSJD1 WILD-TYPE
  0             17              311
  1              0               23
[1] 2 2
[1] FALSE
D13V7, binary
                  cls
clus                 0   1
  FTSJD1 MUTATED    15   9
  FTSJD1 WILD-TYPE 244 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FTSJD1 MUTATED     15    9
  FTSJD1 WILD-TYPE  244  212
        clus
vv       FTSJD1 MUTATED FTSJD1 WILD-TYPE
  FEMALE             15              244
  MALE                9              212
[1] 2 2
[1] FALSE
D13V8, binary
                  cls
clus                 0   1
  FTSJD1 MUTATED    19   1
  FTSJD1 WILD-TYPE 314  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FTSJD1 MUTATED     19    1
  FTSJD1 WILD-TYPE  314   48
     clus
vv    FTSJD1 MUTATED FTSJD1 WILD-TYPE
  NO              19              314
  YES              1               48
[1] 2 2
[1] FALSE
D13V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FTSJD1 MUTATED                            0                                 3
  FTSJD1 WILD-TYPE                         18                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FTSJD1 MUTATED                                                   19
  FTSJD1 WILD-TYPE                                                276
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FTSJD1 MUTATED                                            0
  FTSJD1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FTSJD1 MUTATED                                               0
  FTSJD1 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  FTSJD1 MUTATED                                0
  FTSJD1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  FTSJD1 MUTATED                                    0
  FTSJD1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FTSJD1 MUTATED                              0                             1
  FTSJD1 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FTSJD1 MUTATED                                               1
  FTSJD1 WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  FTSJD1 MUTATED                              0
  FTSJD1 WILD-TYPE                            9
D13V10, multiclass
                                                    clus
vv                                                   FTSJD1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             19
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   FTSJD1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              276
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
D13V12, continuous
                  vv
clus                R0  R1  R2  RX
  FTSJD1 MUTATED    20   0   0   1
  FTSJD1 WILD-TYPE 290  11   4  24
D13V13, multiclass
    clus
vv   FTSJD1 MUTATED FTSJD1 WILD-TYPE
  R0             20              290
  R1              0               11
  R2              0                4
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FTSJD1 MUTATED                                  0     1
  FTSJD1 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FTSJD1 MUTATED                           2    18
  FTSJD1 WILD-TYPE                        27   359
D13V14, multiclass
                                  clus
vv                                 FTSJD1 MUTATED FTSJD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                        18              359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                  cls
clus                 0   1
  FTSJD1 MUTATED     0  20
  FTSJD1 WILD-TYPE   6 329
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FTSJD1 MUTATED      0   20
  FTSJD1 WILD-TYPE    6  329
                        clus
vv                       FTSJD1 MUTATED FTSJD1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             20              329
[1] 2 2
[1] FALSE

Clustering(14) Variable = MET MUTATION ANALYSIS
D14V1, survival
               sevent
clus2             0   1
  MET MUTATED    13   6
  MET WILD-TYPE 289 149
  MET MUTATED MET WILD-TYPE 
           19           438 
  MET MUTATED MET WILD-TYPE 
            6           149 
$`MET MUTATED`
TCGA-05-4403 TCGA-44-2657 TCGA-44-7671 TCGA-44-A47G TCGA-49-6745 TCGA-49-6761 
       19.00        44.42        29.23        11.54        17.16        11.64 
TCGA-50-5930 TCGA-50-5933 TCGA-50-6597 TCGA-55-6712 TCGA-55-6982 TCGA-55-8511 
        9.27        78.67        41.69         0.79        32.71         0.30 
TCGA-64-5781 TCGA-78-7143 TCGA-86-8358 TCGA-91-6847 TCGA-93-7348 TCGA-97-8176 
       51.25       163.10        21.47        27.68        17.46        15.39 
TCGA-J2-A4AE 
       35.47 

$`MET WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 
        0.00         9.96        24.03        47.05         8.02        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 TCGA-44-2665 
       14.73        26.30         4.37        46.98        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        29.00        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.08        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       16.04        53.29        55.33        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       23.05        48.62         2.86         0.07        32.65        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        7.79         2.20        45.34        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36         0.26         0.49        17.72         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
       38.37        87.98         2.04        42.90        28.41        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 
        9.24         1.25        39.09        50.33        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        9.57       104.19       238.29         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.20        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
        2.60        13.71        12.23         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        0.72        18.67        17.92         5.39        18.12        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       18.08        32.48        19.00        14.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  MET MUTATED MET WILD-TYPE 
          0.3           0.0 
  MET MUTATED MET WILD-TYPE 
       163.10        238.29 
  MET MUTATED MET WILD-TYPE 
        21.47         19.79 
[1] "0.3 - 163.1 (21.5)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.4"
D14V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MET MUTATED         0        3       11         1         1          4
  MET WILD-TYPE       4      120      121        46        65         66
               vv
clus            STAGE IIIB STAGE IV
  MET MUTATED            1        0
  MET WILD-TYPE         10       25
D14V3, multiclass
            clus
vv           MET MUTATED MET WILD-TYPE
  STAGE I              0             4
  STAGE IA             3           120
  STAGE IB            11           121
  STAGE IIA            1            46
  STAGE IIB            1            65
  STAGE IIIA           4            66
  STAGE IIIB           1            10
  STAGE IV             0            25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MET MUTATED     4  15   1   1
  MET WILD-TYPE 151 246  42  17
D14V4, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  T1           4           151
  T2          15           246
  T3           1            42
  T4           1            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
  MET MUTATED    13   3     4
  MET WILD-TYPE 294  86    68
D14V5, multiclass
       clus
vv      MET MUTATED MET WILD-TYPE
  N0             13           294
  N1              3            86
  N2+N3           4            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
               cls
clus              0   1
  MET MUTATED    15   0
  MET WILD-TYPE 313  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     15    0
  MET WILD-TYPE  313   23
   clus
vv  MET MUTATED MET WILD-TYPE
  0          15           313
  1           0            23
[1] 2 2
[1] FALSE
D14V7, binary
               cls
clus              0   1
  MET MUTATED    12   9
  MET WILD-TYPE 247 212
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     12    9
  MET WILD-TYPE  247  212
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE          12           247
  MALE             9           212
[1] 2 2
[1] FALSE
D14V8, binary
               cls
clus              0   1
  MET MUTATED    14   4
  MET WILD-TYPE 319  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     14    4
  MET WILD-TYPE  319   45
     clus
vv    MET MUTATED MET WILD-TYPE
  NO           14           319
  YES           4            45
[1] 2 2
[1] FALSE
D14V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MET MUTATED                            1                                 4
  MET WILD-TYPE                         17                                97
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MET MUTATED                                                   15
  MET WILD-TYPE                                                280
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MET MUTATED                                            0
  MET WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MET MUTATED                                               1
  MET WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  MET MUTATED                                0
  MET WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  MET MUTATED                                    0                            0
  MET WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  MET MUTATED                               0
  MET WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MET MUTATED                                               0
  MET WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  MET MUTATED                              0
  MET WILD-TYPE                            9
D14V10, multiclass
                                                    clus
vv                                                   MET MUTATED MET WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          15           280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
D14V12, continuous
               vv
clus             R0  R1  R2  RX
  MET MUTATED    14   0   0   0
  MET WILD-TYPE 296  11   4  25
D14V13, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  R0          14           296
  R1           0            11
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     0
  MET WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           1    17
  MET WILD-TYPE                        28   360
D14V14, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                     17           360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
               cls
clus              0   1
  MET MUTATED     0  14
  MET WILD-TYPE   6 335
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      0   14
  MET WILD-TYPE    6  335
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          14           335
[1] 2 2
[1] FALSE

Clustering(15) Variable = GAGE2A MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  GAGE2A MUTATED     6   2
  GAGE2A WILD-TYPE 296 153
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               8              449 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               2              153 
$`GAGE2A MUTATED`
TCGA-44-2665 TCGA-44-3396 TCGA-44-6147 TCGA-44-6779 TCGA-44-7661 TCGA-55-1592 
       42.77        37.15        27.78        16.44        12.03        23.05 
TCGA-55-8302 TCGA-86-8674 
        0.76        26.50 

$`GAGE2A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       38.10        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
       28.37        28.01        23.77        19.56         9.93        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
       21.63        23.18        63.72        32.45        61.28        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        16.04 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       53.29        55.33        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.09         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12         9.37        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 
       34.29        30.54        13.94        35.21        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42         1.45         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 
       13.91        30.84        27.58         0.62        28.34        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29        41.82        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  GAGE2A MUTATED GAGE2A WILD-TYPE 
            0.76             0.00 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
           42.77           238.29 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
          24.775           19.760 
[1] "0.8 - 42.8 (24.8)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.2"
D15V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GAGE2A MUTATED         0        2        2         1         2          1
  GAGE2A WILD-TYPE       4      121      130        46        64         69
                  vv
clus               STAGE IIIB STAGE IV
  GAGE2A MUTATED            0        0
  GAGE2A WILD-TYPE         11       25
D15V3, multiclass
            clus
vv           GAGE2A MUTATED GAGE2A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                2              130
  STAGE IIA               1               46
  STAGE IIB               2               64
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GAGE2A MUTATED     1   7   0   0
  GAGE2A WILD-TYPE 154 254  43  18
D15V4, multiclass
    clus
vv   GAGE2A MUTATED GAGE2A WILD-TYPE
  T1              1              154
  T2              7              254
  T3              0               43
  T4              0               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
  GAGE2A MUTATED     3   3     1
  GAGE2A WILD-TYPE 304  86    71
D15V5, multiclass
       clus
vv      GAGE2A MUTATED GAGE2A WILD-TYPE
  N0                 3              304
  N1                 3               86
  N2+N3              1               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     6   0
  GAGE2A WILD-TYPE 322  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      6    0
  GAGE2A WILD-TYPE  322   23
   clus
vv  GAGE2A MUTATED GAGE2A WILD-TYPE
  0              6              322
  1              0               23
[1] 2 2
[1] FALSE
D15V7, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     5   3
  GAGE2A WILD-TYPE 254 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      5    3
  GAGE2A WILD-TYPE  254  218
        clus
vv       GAGE2A MUTATED GAGE2A WILD-TYPE
  FEMALE              5              254
  MALE                3              218
[1] 2 2
[1] FALSE
D15V8, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     7   0
  GAGE2A WILD-TYPE 326  49
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      7    0
  GAGE2A WILD-TYPE  326   49
     clus
vv    GAGE2A MUTATED GAGE2A WILD-TYPE
  NO               7              326
  YES              0               49
[1] 2 2
[1] FALSE
D15V9, continuous
[1] "Remove cluster labels:" "GAGE2A MUTATED"        
clus
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               2              115 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-44-3918 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-44-4112       TCGA-44-6144       TCGA-44-6775       TCGA-44-7660 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-44-A47F       TCGA-49-4486       TCGA-49-4494       TCGA-49-4505 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-49-4506       TCGA-49-4510       TCGA-49-6742       TCGA-49-6743 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-49-6744       TCGA-53-7624       TCGA-53-A4EZ       TCGA-55-7283 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-7573       TCGA-55-7725       TCGA-55-7910       TCGA-55-7914 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-8089       TCGA-55-8096       TCGA-55-8205       TCGA-55-8208 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8511       TCGA-55-8512 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-8621       TCGA-55-A48Z 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A491       TCGA-55-A492       TCGA-55-A494 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-62-8394       TCGA-62-8395       TCGA-62-8397       TCGA-62-8398 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O       TCGA-62-A46P 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1681       TCGA-64-5775       TCGA-64-5778 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-69-7974       TCGA-69-8254       TCGA-71-6725       TCGA-71-8520 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-73-4670       TCGA-73-4676       TCGA-73-4677       TCGA-73-7498 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-73-7499       TCGA-75-5122       TCGA-83-5908       TCGA-86-6562 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-6851       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7953       TCGA-86-7954       TCGA-86-7955 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-8054       TCGA-86-8055       TCGA-86-8056       TCGA-86-8073 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8280       TCGA-86-8281       TCGA-86-8358 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6829 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-91-6849       TCGA-93-7347       TCGA-93-7348       TCGA-93-8067 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-95-7567       TCGA-99-7458 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GAGE2A MUTATED                            0                                 0
  GAGE2A WILD-TYPE                         18                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GAGE2A MUTATED                                                    7
  GAGE2A WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GAGE2A MUTATED                                            0
  GAGE2A WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GAGE2A MUTATED                                               0
  GAGE2A WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  GAGE2A MUTATED                                0
  GAGE2A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  GAGE2A MUTATED                                    0
  GAGE2A WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  GAGE2A MUTATED                              0                             1
  GAGE2A WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GAGE2A MUTATED                                               0
  GAGE2A WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  GAGE2A MUTATED                              0
  GAGE2A WILD-TYPE                            9
D15V10, multiclass
                                                    clus
vv                                                   GAGE2A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   GAGE2A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
D15V12, continuous
                  vv
clus                R0  R1  R2  RX
  GAGE2A MUTATED     5   0   0   0
  GAGE2A WILD-TYPE 305  11   4  25
D15V13, multiclass
    clus
vv   GAGE2A MUTATED GAGE2A WILD-TYPE
  R0              5              305
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAGE2A MUTATED                                  0     0
  GAGE2A WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GAGE2A MUTATED                           0     8
  GAGE2A WILD-TYPE                        29   369
D15V14, multiclass
                                  clus
vv                                 GAGE2A MUTATED GAGE2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         8              369
[1] 4 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
  GAGE2A MUTATED     0   6
  GAGE2A WILD-TYPE   6 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      0    6
  GAGE2A WILD-TYPE    6  343
                        clus
vv                       GAGE2A MUTATED GAGE2A WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              343
[1] 2 2
[1] FALSE

Clustering(16) Variable = SETD2 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    14  11
  SETD2 WILD-TYPE 288 144
  SETD2 MUTATED SETD2 WILD-TYPE 
             25             432 
  SETD2 MUTATED SETD2 WILD-TYPE 
             11             144 
$`SETD2 MUTATED`
TCGA-05-4425 TCGA-05-4427 TCGA-38-4631 TCGA-49-4487 TCGA-49-6744 TCGA-50-5941 
       21.99        26.01        11.64        28.11        55.33         9.37 
TCGA-50-5942 TCGA-53-7624 TCGA-55-6986 TCGA-55-A4DF TCGA-62-A46P TCGA-64-5775 
       29.03        34.29       107.21        20.19        19.53         2.04 
TCGA-67-6216 TCGA-69-7760 TCGA-73-4658 TCGA-73-4666 TCGA-73-4676 TCGA-78-7150 
        4.64         6.64        52.60        26.30         9.24        21.90 
TCGA-86-7714 TCGA-86-8278 TCGA-91-6848 TCGA-97-7941 TCGA-97-A4M6 TCGA-97-A4M7 
       20.55        31.04         7.36         0.72        18.67        20.68 
TCGA-MP-A4SY 
       49.35 

$`SETD2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       30.02        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        76.21        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       16.04        53.29        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.09         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        8.45        15.12        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        36.99         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       60.03        24.99        40.54        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       49.25        47.80        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       81.80        38.37        87.98        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        18.84        14.04        14.73         5.72 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
       13.87         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 
        4.24        17.16         2.01         6.90        23.38        82.68 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31        30.31         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        38.04        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
       10.19         2.60        13.71        12.23        27.68         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        5.95         0.59        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 
       21.44        19.76        20.52        17.75        20.84        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.72            0.00 
  SETD2 MUTATED SETD2 WILD-TYPE 
         107.21          238.29 
  SETD2 MUTATED SETD2 WILD-TYPE 
         20.680          19.695 
[1] "0.7 - 107.2 (20.7)" "0.0 - 238.3 (19.7)"
[1] "hr=" "1.3"
D16V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SETD2 MUTATED         0        7        6         2         6          6
  SETD2 WILD-TYPE       4      116      126        45        60         64
                 vv
clus              STAGE IIIB STAGE IV
  SETD2 MUTATED            0        3
  SETD2 WILD-TYPE         11       22
D16V3, multiclass
            clus
vv           SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               7             116
  STAGE IB               6             126
  STAGE IIA              2              45
  STAGE IIB              6              60
  STAGE IIIA             6              64
  STAGE IIIB             0              11
  STAGE IV               3              22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SETD2 MUTATED     9  18   2   1
  SETD2 WILD-TYPE 146 243  41  17
D16V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1             9             146
  T2            18             243
  T3             2              41
  T4             1              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
  SETD2 MUTATED    18   7     5
  SETD2 WILD-TYPE 289  82    67
D16V5, multiclass
       clus
vv      SETD2 MUTATED SETD2 WILD-TYPE
  N0               18             289
  N1                7              82
  N2+N3             5              67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                 cls
clus                0   1
  SETD2 MUTATED    22   3
  SETD2 WILD-TYPE 306  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     22    3
  SETD2 WILD-TYPE  306   20
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            22             306
  1             3              20
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus                0   1
  SETD2 MUTATED    20  10
  SETD2 WILD-TYPE 239 211
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     20   10
  SETD2 WILD-TYPE  239  211
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            20             239
  MALE              10             211
[1] 2 2
[1] FALSE
D16V8, binary
                 cls
clus                0   1
  SETD2 MUTATED    22   4
  SETD2 WILD-TYPE 311  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     22    4
  SETD2 WILD-TYPE  311   45
     clus
vv    SETD2 MUTATED SETD2 WILD-TYPE
  NO             22             311
  YES             4              45
[1] 2 2
[1] FALSE
D16V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SETD2 MUTATED                            2                                 7
  SETD2 WILD-TYPE                         16                                94
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SETD2 MUTATED                                                   19
  SETD2 WILD-TYPE                                                276
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SETD2 MUTATED                                            0
  SETD2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SETD2 MUTATED                                               1
  SETD2 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  SETD2 MUTATED                                0
  SETD2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  SETD2 MUTATED                                    0
  SETD2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SETD2 MUTATED                              0                             1
  SETD2 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SETD2 MUTATED                                               0
  SETD2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  SETD2 MUTATED                              0
  SETD2 WILD-TYPE                            9
D16V10, multiclass
                                                    clus
vv                                                   SETD2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            19
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   SETD2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             276
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
D16V12, continuous
                 vv
clus               R0  R1  R2  RX
  SETD2 MUTATED    23   1   1   0
  SETD2 WILD-TYPE 287  10   3  25
D16V13, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  R0            23             287
  R1             1              10
  R2             1               3
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     0
  SETD2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           1    23
  SETD2 WILD-TYPE                        28   354
D16V14, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       23             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, binary
                 cls
clus                0   1
  SETD2 MUTATED     1  19
  SETD2 WILD-TYPE   5 330
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      1   19
  SETD2 WILD-TYPE    5  330
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            19             330
[1] 2 2
[1] FALSE

Clustering(17) Variable = U2AF1 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  U2AF1 MUTATED     8   3
  U2AF1 WILD-TYPE 294 152
  U2AF1 MUTATED U2AF1 WILD-TYPE 
             11             446 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              3             152 
$`U2AF1 MUTATED`
TCGA-49-4505 TCGA-49-6744 TCGA-50-5941 TCGA-50-8460 TCGA-55-1595 TCGA-55-7727 
       14.07        55.33         9.37        27.25        48.62         1.12 
TCGA-55-7903 TCGA-78-7145 TCGA-78-8655 TCGA-86-8585 TCGA-MP-A4T4 
       18.64        27.16        77.59         1.15        86.04 

$`U2AF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        46.72        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
       29.46        29.75        55.89        16.04        53.29        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       40.60        78.67        21.47         8.45        15.12        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        34.29        30.54        13.94        35.21        23.05 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7907 TCGA-55-7910 
        1.28         0.79         1.78         1.45         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 
        9.24         1.25        39.09        50.33       163.10         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        9.57       104.19       238.29         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
       50.24       232.18        39.75        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        21.47        14.60        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        49.35        37.35        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  U2AF1 MUTATED U2AF1 WILD-TYPE 
           1.12            0.00 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
          86.04          238.29 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
          27.16           19.79 
[1] "1.1 - 86.0 (27.2)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.8"
D17V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  U2AF1 MUTATED         0        4        1         1         2          2
  U2AF1 WILD-TYPE       4      119      131        46        64         68
                 vv
clus              STAGE IIIB STAGE IV
  U2AF1 MUTATED            0        1
  U2AF1 WILD-TYPE         11       24
D17V3, multiclass
            clus
vv           U2AF1 MUTATED U2AF1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               1             131
  STAGE IIA              1              46
  STAGE IIB              2              64
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  U2AF1 MUTATED     5   5   0   1
  U2AF1 WILD-TYPE 150 256  43  17
D17V4, multiclass
    clus
vv   U2AF1 MUTATED U2AF1 WILD-TYPE
  T1             5             150
  T2             5             256
  T3             0              43
  T4             1              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
  U2AF1 MUTATED     5   4     2
  U2AF1 WILD-TYPE 302  85    70
D17V5, multiclass
       clus
vv      U2AF1 MUTATED U2AF1 WILD-TYPE
  N0                5             302
  N1                4              85
  N2+N3             2              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                 cls
clus                0   1
  U2AF1 MUTATED     7   1
  U2AF1 WILD-TYPE 321  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      7    1
  U2AF1 WILD-TYPE  321   22
   clus
vv  U2AF1 MUTATED U2AF1 WILD-TYPE
  0             7             321
  1             1              22
[1] 2 2
[1] FALSE
D17V7, binary
                 cls
clus                0   1
  U2AF1 MUTATED     7   4
  U2AF1 WILD-TYPE 252 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      7    4
  U2AF1 WILD-TYPE  252  217
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  FEMALE             7             252
  MALE               4             217
[1] 2 2
[1] FALSE
D17V8, binary
                 cls
clus                0   1
  U2AF1 MUTATED     7   1
  U2AF1 WILD-TYPE 326  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      7    1
  U2AF1 WILD-TYPE  326   48
     clus
vv    U2AF1 MUTATED U2AF1 WILD-TYPE
  NO              7             326
  YES             1              48
[1] 2 2
[1] FALSE
D17V9, continuous
[1] "Remove cluster labels:" "U2AF1 MUTATED"         
clus
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              2             115 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-44-3396 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-6144      TCGA-44-6147 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-44-A47F      TCGA-49-4486 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-49-4494      TCGA-49-4506      TCGA-49-4510      TCGA-49-6742 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-49-6743      TCGA-53-7624      TCGA-53-A4EZ      TCGA-55-7283 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-8621      TCGA-55-A48Z 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A491      TCGA-55-A492      TCGA-55-A494 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5775      TCGA-64-5778 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-73-4670      TCGA-73-4676      TCGA-73-4677      TCGA-73-7498 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-73-7499      TCGA-75-5122      TCGA-83-5908      TCGA-86-6562 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-6851      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7953      TCGA-86-7954      TCGA-86-7955 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-8054      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8280      TCGA-86-8281      TCGA-86-8358 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-91-6849      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567      TCGA-99-7458 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  U2AF1 MUTATED                            0                                 2
  U2AF1 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  U2AF1 MUTATED                                                    6
  U2AF1 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  U2AF1 MUTATED                                            0
  U2AF1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  U2AF1 MUTATED                                               0
  U2AF1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  U2AF1 MUTATED                                1
  U2AF1 WILD-TYPE                              1
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  U2AF1 MUTATED                                    0
  U2AF1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  U2AF1 MUTATED                              0                             1
  U2AF1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  U2AF1 MUTATED                                               1
  U2AF1 WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  U2AF1 MUTATED                              0
  U2AF1 WILD-TYPE                            9
D17V10, multiclass
                                                    clus
vv                                                   U2AF1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   U2AF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
D17V12, continuous
                 vv
clus               R0  R1  R2  RX
  U2AF1 MUTATED     8   1   0   0
  U2AF1 WILD-TYPE 302  10   4  25
D17V13, multiclass
    clus
vv   U2AF1 MUTATED U2AF1 WILD-TYPE
  R0             8             302
  R1             1              10
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  U2AF1 MUTATED                                  0     1
  U2AF1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  U2AF1 MUTATED                           0     9
  U2AF1 WILD-TYPE                        29   368
D17V14, multiclass
                                  clus
vv                                 U2AF1 MUTATED U2AF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, binary
                 cls
clus                0   1
  U2AF1 MUTATED     0   6
  U2AF1 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      0    6
  U2AF1 WILD-TYPE    6  343
                        clus
vv                       U2AF1 MUTATED U2AF1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(18) Variable = ERBB2 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED     7   4
  ERBB2 WILD-TYPE 295 151
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             446 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4             151 
$`ERBB2 MUTATED`
TCGA-05-4384 TCGA-05-4434 TCGA-05-5715 TCGA-38-4629 TCGA-44-2656 TCGA-44-3396 
       14.01        15.02         2.04        28.41        46.98        37.15 
TCGA-44-3919 TCGA-44-A47B TCGA-86-6562 TCGA-86-A456 TCGA-95-7567 
       33.73         9.44        12.36        29.46        18.67 

$`ERBB2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-4122 
       15.02         4.96        29.00        22.03         9.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 
       44.42        38.10        42.77        38.24        34.06        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.98        15.32        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24        17.16         2.01         6.90        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        50.33       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        9.57       104.19       238.29         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 
       27.58         0.62        28.34        26.50        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       41.82        16.54         2.86        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        6.35        10.09        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           2.04            0.00 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          46.98          238.29 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          18.67           19.82 
[1] "2.0 - 47.0 (18.7)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.3"
D18V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ERBB2 MUTATED         0        2        3         1         2          2
  ERBB2 WILD-TYPE       4      121      129        46        64         68
                 vv
clus              STAGE IIIB STAGE IV
  ERBB2 MUTATED            0        1
  ERBB2 WILD-TYPE         11       24
D18V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               3             129
  STAGE IIA              1              46
  STAGE IIB              2              64
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB2 MUTATED     2   7   1   1
  ERBB2 WILD-TYPE 153 254  42  17
D18V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             2             153
  T2             7             254
  T3             1              42
  T4             1              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
  ERBB2 MUTATED     6   3     2
  ERBB2 WILD-TYPE 301  86    70
D18V5, multiclass
       clus
vv      ERBB2 MUTATED ERBB2 WILD-TYPE
  N0                6             301
  N1                3              86
  N2+N3             2              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                 cls
clus                0   1
  ERBB2 MUTATED    10   1
  ERBB2 WILD-TYPE 318  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     10    1
  ERBB2 WILD-TYPE  318   22
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0            10             318
  1             1              22
[1] 2 2
[1] FALSE
D18V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED     5   6
  ERBB2 WILD-TYPE 254 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      5    6
  ERBB2 WILD-TYPE  254  215
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             5             254
  MALE               6             215
[1] 2 2
[1] FALSE
D18V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED     8   1
  ERBB2 WILD-TYPE 325  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      8    1
  ERBB2 WILD-TYPE  325   48
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO              8             325
  YES             1              48
[1] 2 2
[1] FALSE
D18V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ERBB2 MUTATED                            0                                 4
  ERBB2 WILD-TYPE                         18                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ERBB2 MUTATED                                                    6
  ERBB2 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ERBB2 MUTATED                                            0
  ERBB2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ERBB2 MUTATED                                               0
  ERBB2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ERBB2 MUTATED                                0
  ERBB2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ERBB2 MUTATED                                    0
  ERBB2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ERBB2 MUTATED                              0                             1
  ERBB2 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ERBB2 MUTATED                                               0
  ERBB2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ERBB2 MUTATED                              0
  ERBB2 WILD-TYPE                            9
D18V10, multiclass
                                                    clus
vv                                                   ERBB2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ERBB2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
D18V12, continuous
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED     7   0   1   1
  ERBB2 WILD-TYPE 303  11   3  24
D18V13, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             1               3
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB2 MUTATED                                  0     1
  ERBB2 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED                           0     7
  ERBB2 WILD-TYPE                        29   370
D18V14, multiclass
                                  clus
vv                                 ERBB2 MUTATED ERBB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, binary
                 cls
clus                0   1
  ERBB2 MUTATED     0   8
  ERBB2 WILD-TYPE   6 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      0    8
  ERBB2 WILD-TYPE    6  341
                        clus
vv                       ERBB2 MUTATED ERBB2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             341
[1] 2 2
[1] FALSE

Clustering(19) Variable = CDKN2A MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    13   3
  CDKN2A WILD-TYPE 289 152
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              441 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               3              152 
$`CDKN2A MUTATED`
TCGA-05-4426 TCGA-05-4433 TCGA-38-4625 TCGA-44-5645 TCGA-44-7662 TCGA-49-4505 
       26.01        24.00        97.74        28.01         7.17        14.07 
TCGA-50-6595 TCGA-53-A4EZ TCGA-55-8089 TCGA-55-8205 TCGA-55-A492 TCGA-67-3771 
        6.21        35.21         3.29         1.08        19.59        20.05 
TCGA-78-7148 TCGA-86-8585 TCGA-93-8067 TCGA-97-8547 
       20.58         1.15         6.12        21.60 

$`CDKN2A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 
       30.02        21.99        26.01        25.02        25.02        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46        12.03        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 
       28.11        28.57        12.66        35.54        46.72        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.33        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 
        3.91        25.55        11.05        12.16        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1.58        20.58         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       51.25        28.47        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        17.16         2.01         6.90 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        82.68        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        19.27       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       31.04        31.20        23.05        21.47        14.60        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX 
       18.12        15.39        16.41        14.30        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1.08             0.00 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           97.74           238.29 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           19.82            19.82 
[1] "1.1 - 97.7 (19.8)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.4"
D19V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CDKN2A MUTATED         0        4        6         1         3          2
  CDKN2A WILD-TYPE       4      119      126        46        63         68
                  vv
clus               STAGE IIIB STAGE IV
  CDKN2A MUTATED            0        0
  CDKN2A WILD-TYPE         11       25
D19V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              119
  STAGE IB                6              126
  STAGE IIA               1               46
  STAGE IIB               3               63
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CDKN2A MUTATED     4  12   0   0
  CDKN2A WILD-TYPE 151 249  43  18
D19V4, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  T1              4              151
  T2             12              249
  T3              0               43
  T4              0               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
  CDKN2A MUTATED    10   3     2
  CDKN2A WILD-TYPE 297  86    70
D19V5, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  N0                10              297
  N1                 3               86
  N2+N3              2               70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    10   0
  CDKN2A WILD-TYPE 318  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     10    0
  CDKN2A WILD-TYPE  318   23
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             10              318
  1              0               23
[1] 2 2
[1] FALSE
D19V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     8   8
  CDKN2A WILD-TYPE 251 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      8    8
  CDKN2A WILD-TYPE  251  213
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              8              251
  MALE                8              213
[1] 2 2
[1] FALSE
D19V8, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     8   2
  CDKN2A WILD-TYPE 325  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      8    2
  CDKN2A WILD-TYPE  325   47
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO               8              325
  YES              2               47
[1] 2 2
[1] FALSE
D19V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CDKN2A MUTATED                            1                                 4
  CDKN2A WILD-TYPE                         17                                97
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CDKN2A MUTATED                                                   10
  CDKN2A WILD-TYPE                                                285
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CDKN2A MUTATED                                            0
  CDKN2A WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CDKN2A MUTATED                                               0
  CDKN2A WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CDKN2A MUTATED                                0
  CDKN2A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CDKN2A MUTATED                                    0
  CDKN2A WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CDKN2A MUTATED                              0                             0
  CDKN2A WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CDKN2A MUTATED                                               1
  CDKN2A WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CDKN2A MUTATED                              0
  CDKN2A WILD-TYPE                            9
D19V10, multiclass
                                                    clus
vv                                                   CDKN2A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CDKN2A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
D19V12, continuous
                  vv
clus                R0  R1  R2  RX
  CDKN2A MUTATED    10   0   0   2
  CDKN2A WILD-TYPE 300  11   4  23
D19V13, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0             10              300
  R1              0               11
  R2              0                4
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKN2A MUTATED                                  0     1
  CDKN2A WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED                           2    10
  CDKN2A WILD-TYPE                        27   367
D19V14, multiclass
                                  clus
vv                                 CDKN2A MUTATED CDKN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                        10              367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     1  11
  CDKN2A WILD-TYPE   5 338
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1   11
  CDKN2A WILD-TYPE    5  338
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             11              338
[1] 2 2
[1] FALSE

Clustering(20) Variable = SRPX MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  SRPX MUTATED     9   5
  SRPX WILD-TYPE 293 150
  SRPX MUTATED SRPX WILD-TYPE 
            14            443 
  SRPX MUTATED SRPX WILD-TYPE 
             5            150 
$`SRPX MUTATED`
TCGA-05-4390 TCGA-05-4432 TCGA-38-4628 TCGA-44-2665 TCGA-44-3396 TCGA-44-7659 
       37.02        25.02        49.05        42.77        37.15        22.72 
TCGA-49-4514 TCGA-50-6593 TCGA-78-7155 TCGA-93-7348 TCGA-95-7043 TCGA-97-7938 
       55.89        11.05        38.50        17.46        16.54         0.59 
TCGA-97-A4LX TCGA-97-A4M6 
       20.19        18.67 

$`SRPX WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-3398 TCGA-44-3918 
        4.37        46.98        44.42        38.10        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 
       63.72        32.45        61.28        16.44        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24        17.16         2.01         6.90        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        50.33       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       22.45         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       41.82         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
       64.60        63.52        43.79        25.48         5.95         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       14.30        21.60        20.58        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       17.75        20.84        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  SRPX MUTATED SRPX WILD-TYPE 
          0.59           0.00 
  SRPX MUTATED SRPX WILD-TYPE 
         55.89         238.29 
  SRPX MUTATED SRPX WILD-TYPE 
         23.87          19.73 
[1] "0.6 - 55.9 (23.9)"  "0.0 - 238.3 (19.7)"
[1] "hr=" "1.1"
D20V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SRPX MUTATED         0        6        3         0         3          2
  SRPX WILD-TYPE       4      117      129        47        63         68
                vv
clus             STAGE IIIB STAGE IV
  SRPX MUTATED            0        0
  SRPX WILD-TYPE         11       25
D20V3, multiclass
            clus
vv           SRPX MUTATED SRPX WILD-TYPE
  STAGE I               0              4
  STAGE IA              6            117
  STAGE IB              3            129
  STAGE IIA             0             47
  STAGE IIB             3             63
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SRPX MUTATED     7   7   0   0
  SRPX WILD-TYPE 148 254  43  18
D20V4, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  T1            7            148
  T2            7            254
  T3            0             43
  T4            0             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
  SRPX MUTATED     9   3     2
  SRPX WILD-TYPE 298  86    70
D20V5, multiclass
       clus
vv      SRPX MUTATED SRPX WILD-TYPE
  N0               9            298
  N1               3             86
  N2+N3            2             70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                cls
clus               0   1
  SRPX MUTATED    10   0
  SRPX WILD-TYPE 318  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED     10    0
  SRPX WILD-TYPE  318   23
   clus
vv  SRPX MUTATED SRPX WILD-TYPE
  0           10            318
  1            0             23
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus               0   1
  SRPX MUTATED    10   4
  SRPX WILD-TYPE 249 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED     10    4
  SRPX WILD-TYPE  249  217
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  FEMALE           10            249
  MALE              4            217
[1] 2 2
[1] FALSE
D20V8, binary
                cls
clus               0   1
  SRPX MUTATED    12   1
  SRPX WILD-TYPE 321  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED     12    1
  SRPX WILD-TYPE  321   48
     clus
vv    SRPX MUTATED SRPX WILD-TYPE
  NO            12            321
  YES            1             48
[1] 2 2
[1] FALSE
D20V9, continuous
[1] "Remove cluster labels:" "SRPX MUTATED"          
clus
  SRPX MUTATED SRPX WILD-TYPE 
             2            115 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-44-3918 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-44-4112     TCGA-44-6144     TCGA-44-6147     TCGA-44-6775 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-44-7660     TCGA-44-A47F     TCGA-49-4486     TCGA-49-4494 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4510     TCGA-49-6742 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-49-6743     TCGA-49-6744     TCGA-53-7624     TCGA-53-A4EZ 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-8621 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5775 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4676     TCGA-73-4677 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-6562     TCGA-86-6851     TCGA-86-7701     TCGA-86-7711 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7953     TCGA-86-7954 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-7955     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8280     TCGA-86-8281 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6849     TCGA-93-7347     TCGA-93-8067 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-95-7567     TCGA-99-7458 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SRPX MUTATED                            0                                 6
  SRPX WILD-TYPE                         18                                95
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SRPX MUTATED                                                    6
  SRPX WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SRPX MUTATED                                            0
  SRPX WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SRPX MUTATED                                               1
  SRPX WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SRPX MUTATED                                0
  SRPX WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SRPX MUTATED                                    0
  SRPX WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SRPX MUTATED                              0                             1
  SRPX WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SRPX MUTATED                                               0
  SRPX WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SRPX MUTATED                              0
  SRPX WILD-TYPE                            9
D20V10, multiclass
                                                    clus
vv                                                   SRPX MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SRPX WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
D20V12, continuous
                vv
clus              R0  R1  R2  RX
  SRPX MUTATED    10   0   0   0
  SRPX WILD-TYPE 300  11   4  25
D20V13, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  R0           10            300
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRPX MUTATED                                  0     0
  SRPX WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SRPX MUTATED                           0    12
  SRPX WILD-TYPE                        29   365
D20V14, multiclass
                                  clus
vv                                 SRPX MUTATED SRPX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                      12            365
[1] 4 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
  SRPX MUTATED     0  10
  SRPX WILD-TYPE   6 339
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      0   10
  SRPX WILD-TYPE    6  339
                        clus
vv                       SRPX MUTATED SRPX WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           10            339
[1] 2 2
[1] FALSE

Clustering(21) Variable = ATM MUTATION ANALYSIS
D21V1, survival
               sevent
clus2             0   1
  ATM MUTATED    25  14
  ATM WILD-TYPE 277 141
  ATM MUTATED ATM WILD-TYPE 
           39           418 
  ATM MUTATED ATM WILD-TYPE 
           14           141 
$`ATM MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4417 TCGA-49-4486 TCGA-49-4507 TCGA-49-4510 
       19.96        37.02        14.96        76.21         8.81        29.46 
TCGA-53-7624 TCGA-53-7813 TCGA-55-1595 TCGA-55-6642 TCGA-55-6971 TCGA-55-7815 
       34.29        13.94        48.62        32.65         0.82         1.78 
TCGA-55-8508 TCGA-62-8398 TCGA-62-A46Y TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
        0.49        14.60        13.61        38.37        87.98         2.04 
TCGA-67-6215 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8255 
        5.72         7.56         4.41         2.93        14.01         4.24 
TCGA-73-4659 TCGA-78-7156 TCGA-78-7159 TCGA-78-7539 TCGA-86-8054 TCGA-86-A4JF 
       23.38        32.09        64.90        26.01        37.74        24.23 
TCGA-93-A4JN TCGA-95-7567 TCGA-95-A4VP TCGA-97-8176 TCGA-97-A4M3 TCGA-L9-A443 
       23.61        18.67        19.89        15.39        17.75         6.35 
TCGA-MN-A4N4 TCGA-MP-A4TI TCGA-NJ-A4YP 
       38.63        14.10         1.64 

$`ATM WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        45.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       14.07        32.84        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.33        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        0.72        10.13        36.99         7.59        27.25        30.54 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       35.21        23.05         2.86         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.28         1.12         0.79         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.26        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       54.35        67.96        72.30        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       56.81        20.65        81.80        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6216 
       28.47        20.05        18.84        14.04        14.73         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7974 TCGA-69-7980 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
        6.05        12.56        13.45        17.16         2.01         6.90 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       52.60        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 
      119.51        19.50        38.50         5.88        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        8.02        53.33        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        35.24         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       28.34        26.50        29.46        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       18.18        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       18.12        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        19.76        20.52        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       10.09        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ 
       19.13        73.91        71.05        62.60         0.13        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  ATM MUTATED ATM WILD-TYPE 
         0.49          0.00 
  ATM MUTATED ATM WILD-TYPE 
        87.98        238.29 
  ATM MUTATED ATM WILD-TYPE 
        17.75         19.82 
[1] "0.5 - 88.0 (17.8)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.2"
D21V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ATM MUTATED         0        9       11         4         6          7
  ATM WILD-TYPE       4      114      121        43        60         63
               vv
clus            STAGE IIIB STAGE IV
  ATM MUTATED            1        4
  ATM WILD-TYPE         10       21
D21V3, multiclass
            clus
vv           ATM MUTATED ATM WILD-TYPE
  STAGE I              0             4
  STAGE IA             9           114
  STAGE IB            11           121
  STAGE IIA            4            43
  STAGE IIB            6            60
  STAGE IIIA           7            63
  STAGE IIIB           1            10
  STAGE IV             4            21
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ATM MUTATED    10  26   3   3
  ATM WILD-TYPE 145 235  40  15
D21V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1          10           145
  T2          26           235
  T3           3            40
  T4           3            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
  ATM MUTATED    25  11     5
  ATM WILD-TYPE 282  78    67
D21V5, multiclass
       clus
vv      ATM MUTATED ATM WILD-TYPE
  N0             25           282
  N1             11            78
  N2+N3           5            67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
               cls
clus              0   1
  ATM MUTATED    30   4
  ATM WILD-TYPE 298  19
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     30    4
  ATM WILD-TYPE  298   19
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          30           298
  1           4            19
[1] 2 2
[1] FALSE
D21V7, binary
               cls
clus              0   1
  ATM MUTATED    22  20
  ATM WILD-TYPE 237 201
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     22   20
  ATM WILD-TYPE  237  201
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE          22           237
  MALE            20           201
[1] 2 2
[1] FALSE
D21V8, binary
               cls
clus              0   1
  ATM MUTATED    30   4
  ATM WILD-TYPE 303  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     30    4
  ATM WILD-TYPE  303   45
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO           30           303
  YES           4            45
[1] 2 2
[1] FALSE
D21V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ATM MUTATED                            5                                13
  ATM WILD-TYPE                         13                                88
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ATM MUTATED                                                   19
  ATM WILD-TYPE                                                276
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ATM MUTATED                                            0
  ATM WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ATM MUTATED                                               1
  ATM WILD-TYPE                                            18
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  ATM MUTATED                                1
  ATM WILD-TYPE                              1
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  ATM MUTATED                                    0                            0
  ATM WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  ATM MUTATED                               1
  ATM WILD-TYPE                            21
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ATM MUTATED                                               1
  ATM WILD-TYPE                                             4
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  ATM MUTATED                              1
  ATM WILD-TYPE                            8
D21V10, multiclass
                                                    clus
vv                                                   ATM MUTATED ATM WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   5            13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           13            88
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          19           276
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                1            18
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                1            21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                1             4
  MUCINOUS (COLLOID) CARCINOMA                                 1             8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
D21V12, continuous
               vv
clus             R0  R1  R2  RX
  ATM MUTATED    29   0   0   2
  ATM WILD-TYPE 281  11   4  23
D21V13, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0          29           281
  R1           0            11
  R2           0             4
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATM MUTATED                                  0     1
  ATM WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED                           3    31
  ATM WILD-TYPE                        26   346
D21V14, multiclass
                                  clus
vv                                 ATM MUTATED ATM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  3            26
  WHITE                                     31           346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V15, binary
               cls
clus              0   1
  ATM MUTATED     2  27
  ATM WILD-TYPE   4 322
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      2   27
  ATM WILD-TYPE    4  322
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               2             4
  NOT HISPANIC OR LATINO          27           322
[1] 2 2
[1] FALSE

Clustering(22) Variable = TCEAL5 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  TCEAL5 MUTATED    10   1
  TCEAL5 WILD-TYPE 292 154
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              11              446 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               1              154 
$`TCEAL5 MUTATED`
TCGA-44-5644 TCGA-44-6144 TCGA-44-6776 TCGA-49-6767 TCGA-50-8457 TCGA-53-A4EZ 
       28.37        23.77        63.72        22.26        36.99        35.21 
TCGA-55-7574 TCGA-55-8507 TCGA-73-4662 TCGA-86-8073 TCGA-MP-A4T4 
        3.12         0.26        82.68        24.33        86.04 

$`TCEAL5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       26.56        33.30        28.01        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69         0.72        10.13         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       34.29        30.54        13.94        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24        17.16         2.01         6.90        52.60        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        49.35        37.35        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
            0.26             0.00 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
           86.04           238.29 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
          28.370           19.625 
[1] "0.3 - 86.0 (28.4)"  "0.0 - 238.3 (19.6)"
[1] "hr=" "6"  
D22V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TCEAL5 MUTATED         0        5        3         1         3          1
  TCEAL5 WILD-TYPE       4      118      129        46        63         69
                  vv
clus               STAGE IIIB STAGE IV
  TCEAL5 MUTATED            0        0
  TCEAL5 WILD-TYPE         11       25
D22V3, multiclass
            clus
vv           TCEAL5 MUTATED TCEAL5 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                5              118
  STAGE IB                3              129
  STAGE IIA               1               46
  STAGE IIB               3               63
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TCEAL5 MUTATED     5   7   1   0
  TCEAL5 WILD-TYPE 150 254  42  18
D22V4, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  T1              5              150
  T2              7              254
  T3              1               42
  T4              0               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
  TCEAL5 MUTATED     9   3     1
  TCEAL5 WILD-TYPE 298  86    71
D22V5, multiclass
       clus
vv      TCEAL5 MUTATED TCEAL5 WILD-TYPE
  N0                 9              298
  N1                 3               86
  N2+N3              1               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     8   0
  TCEAL5 WILD-TYPE 320  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      8    0
  TCEAL5 WILD-TYPE  320   23
   clus
vv  TCEAL5 MUTATED TCEAL5 WILD-TYPE
  0              8              320
  1              0               23
[1] 2 2
[1] FALSE
D22V7, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     8   5
  TCEAL5 WILD-TYPE 251 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      8    5
  TCEAL5 WILD-TYPE  251  216
        clus
vv       TCEAL5 MUTATED TCEAL5 WILD-TYPE
  FEMALE              8              251
  MALE                5              216
[1] 2 2
[1] FALSE
D22V8, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     9   1
  TCEAL5 WILD-TYPE 324  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      9    1
  TCEAL5 WILD-TYPE  324   48
     clus
vv    TCEAL5 MUTATED TCEAL5 WILD-TYPE
  NO               9              324
  YES              1               48
[1] 2 2
[1] FALSE
D22V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TCEAL5 MUTATED                            1                                 1
  TCEAL5 WILD-TYPE                         17                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TCEAL5 MUTATED                                                   10
  TCEAL5 WILD-TYPE                                                285
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TCEAL5 MUTATED                                            0
  TCEAL5 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TCEAL5 MUTATED                                               1
  TCEAL5 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  TCEAL5 MUTATED                                0
  TCEAL5 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  TCEAL5 MUTATED                                    0
  TCEAL5 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TCEAL5 MUTATED                              0                             0
  TCEAL5 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TCEAL5 MUTATED                                               0
  TCEAL5 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  TCEAL5 MUTATED                              0
  TCEAL5 WILD-TYPE                            9
D22V10, multiclass
                                                    clus
vv                                                   TCEAL5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   TCEAL5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
D22V12, continuous
                  vv
clus                R0  R1  R2  RX
  TCEAL5 MUTATED     7   1   0   2
  TCEAL5 WILD-TYPE 303  10   4  23
D22V13, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  R0              7              303
  R1              1               10
  R2              0                4
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCEAL5 MUTATED                                  0     0
  TCEAL5 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TCEAL5 MUTATED                           1    10
  TCEAL5 WILD-TYPE                        28   367
D22V14, multiclass
                                  clus
vv                                 TCEAL5 MUTATED TCEAL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        10              367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V15, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     1   7
  TCEAL5 WILD-TYPE   5 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      1    7
  TCEAL5 WILD-TYPE    5  342
                        clus
vv                       TCEAL5 MUTATED TCEAL5 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              7              342
[1] 2 2
[1] FALSE

Clustering(23) Variable = PPP3CA MUTATION ANALYSIS
D23V1, survival
                  sevent
clus2                0   1
  PPP3CA MUTATED    10   2
  PPP3CA WILD-TYPE 292 153
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              445 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
               2              153 
$`PPP3CA MUTATED`
TCGA-05-4422 TCGA-44-5643 TCGA-55-8085 TCGA-55-8514 TCGA-73-4676 TCGA-78-8662 
       12.00        33.30        29.72         6.64         9.24       110.50 
TCGA-86-8585 TCGA-91-8496 TCGA-J2-8194 TCGA-MN-A4N5 TCGA-MP-A5C7 TCGA-NJ-A4YP 
        1.15        16.60        23.80         2.76        73.91         1.64 

$`PPP3CA WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 
       20.05         2.99        14.96         9.01        29.98        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15        19.82         0.16        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.30         0.10         4.80        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31        30.31         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        7.36         1.15        16.18        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29        41.82        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45        21.57        24.30        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF 
       29.46        11.05        24.36        14.10        19.13        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  PPP3CA MUTATED PPP3CA WILD-TYPE 
            1.15             0.00 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
          110.50           238.29 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
           14.30            19.82 
[1] "1.1 - 110.5 (14.3)" "0.0 - 238.3 (19.8)"
[1] "hr=" "2.3"
D23V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PPP3CA MUTATED         0        2        7         1         1          1
  PPP3CA WILD-TYPE       4      121      125        46        65         69
                  vv
clus               STAGE IIIB STAGE IV
  PPP3CA MUTATED            0        0
  PPP3CA WILD-TYPE         11       25
D23V3, multiclass
            clus
vv           PPP3CA MUTATED PPP3CA WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                7              125
  STAGE IIA               1               46
  STAGE IIB               1               65
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PPP3CA MUTATED     2   9   1   0
  PPP3CA WILD-TYPE 153 252  42  18
D23V4, multiclass
    clus
vv   PPP3CA MUTATED PPP3CA WILD-TYPE
  T1              2              153
  T2              9              252
  T3              1               42
  T4              0               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
  PPP3CA MUTATED     9   1     1
  PPP3CA WILD-TYPE 298  88    71
D23V5, multiclass
       clus
vv      PPP3CA MUTATED PPP3CA WILD-TYPE
  N0                 9              298
  N1                 1               88
  N2+N3              1               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     9   0
  PPP3CA WILD-TYPE 319  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      9    0
  PPP3CA WILD-TYPE  319   23
   clus
vv  PPP3CA MUTATED PPP3CA WILD-TYPE
  0              9              319
  1              0               23
[1] 2 2
[1] FALSE
D23V7, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     5   7
  PPP3CA WILD-TYPE 254 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      5    7
  PPP3CA WILD-TYPE  254  214
        clus
vv       PPP3CA MUTATED PPP3CA WILD-TYPE
  FEMALE              5              254
  MALE                7              214
[1] 2 2
[1] FALSE
D23V8, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     7   3
  PPP3CA WILD-TYPE 326  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      7    3
  PPP3CA WILD-TYPE  326   46
     clus
vv    PPP3CA MUTATED PPP3CA WILD-TYPE
  NO               7              326
  YES              3               46
[1] 2 2
[1] FALSE
D23V9, continuous
[1] "Remove cluster labels:" "PPP3CA MUTATED"        
clus
  PPP3CA MUTATED PPP3CA WILD-TYPE 
               2              115 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-44-3396 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-44-3918       TCGA-44-4112       TCGA-44-6144       TCGA-44-6147 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-44-6775       TCGA-44-7660       TCGA-44-A47F       TCGA-49-4486 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-49-4494       TCGA-49-4505       TCGA-49-4506       TCGA-49-4510 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-49-6742       TCGA-49-6743       TCGA-49-6744       TCGA-53-7624 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-53-A4EZ       TCGA-55-7283       TCGA-55-7573       TCGA-55-7725 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-7910       TCGA-55-7914       TCGA-55-8089       TCGA-55-8096 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-8205       TCGA-55-8208       TCGA-55-8507       TCGA-55-8508 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-8511       TCGA-55-8512       TCGA-55-8619       TCGA-55-8620 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-8621       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-A492       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-64-5775       TCGA-64-5778       TCGA-69-7974       TCGA-69-8254 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-71-6725       TCGA-71-8520       TCGA-73-4659       TCGA-73-4662 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-73-4666       TCGA-73-4668       TCGA-73-4670       TCGA-73-4677 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-6562       TCGA-86-6851       TCGA-86-7701       TCGA-86-7711 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7953       TCGA-86-7954 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-7955       TCGA-86-8054       TCGA-86-8055       TCGA-86-8056 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8073       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8280       TCGA-86-8281 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8668       TCGA-86-8669 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8671       TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-91-6829       TCGA-91-6849       TCGA-93-7347       TCGA-93-7348 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-95-7567 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-99-7458       TCGA-MN-A4N1       TCGA-MN-A4N4 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PPP3CA MUTATED                            0                                 2
  PPP3CA WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PPP3CA MUTATED                                                    6
  PPP3CA WILD-TYPE                                                289
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PPP3CA MUTATED                                            0
  PPP3CA WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PPP3CA MUTATED                                               1
  PPP3CA WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  PPP3CA MUTATED                                0
  PPP3CA WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  PPP3CA MUTATED                                    0
  PPP3CA WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PPP3CA MUTATED                              0                             2
  PPP3CA WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PPP3CA MUTATED                                               1
  PPP3CA WILD-TYPE                                             4
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  PPP3CA MUTATED                              0
  PPP3CA WILD-TYPE                            9
D23V10, multiclass
                                                    clus
vv                                                   PPP3CA MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   PPP3CA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
D23V12, continuous
                  vv
clus                R0  R1  R2  RX
  PPP3CA MUTATED     8   0   0   0
  PPP3CA WILD-TYPE 302  11   4  25
D23V13, multiclass
    clus
vv   PPP3CA MUTATED PPP3CA WILD-TYPE
  R0              8              302
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP3CA MUTATED                                  0     0
  PPP3CA WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PPP3CA MUTATED                           2     8
  PPP3CA WILD-TYPE                        27   369
D23V14, multiclass
                                  clus
vv                                 PPP3CA MUTATED PPP3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     2               27
  WHITE                                         8              369
[1] 4 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
  PPP3CA MUTATED     0  10
  PPP3CA WILD-TYPE   6 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      0   10
  PPP3CA WILD-TYPE    6  339
                        clus
vv                       PPP3CA MUTATED PPP3CA WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10              339
[1] 2 2
[1] FALSE

Clustering(24) Variable = FCRLA MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  FCRLA MUTATED    10   4
  FCRLA WILD-TYPE 292 151
  FCRLA MUTATED FCRLA WILD-TYPE 
             14             443 
  FCRLA MUTATED FCRLA WILD-TYPE 
              4             151 
$`FCRLA MUTATED`
TCGA-44-2656 TCGA-44-A479 TCGA-50-5933 TCGA-50-6593 TCGA-50-6594 TCGA-55-6970 
       46.98        15.98        78.67        11.05        12.16        15.25 
TCGA-55-7576 TCGA-55-8089 TCGA-69-7973 TCGA-91-8499 TCGA-91-A4BC TCGA-95-A4VN 
        1.32         3.29         7.56         1.18         1.45        18.18 
TCGA-99-7458 TCGA-MN-A4N5 
       24.56         2.76 

$`FCRLA WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       40.60        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 
       25.12        22.55        42.35         3.91        25.55         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94        35.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         3.12        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
        6.64         6.12        22.68        13.61         5.42         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.18        16.60        14.27        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       27.29         2.76        21.40        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 
       20.52        17.75        20.84        18.67        20.68        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19        38.63        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  FCRLA MUTATED FCRLA WILD-TYPE 
           1.18            0.00 
  FCRLA MUTATED FCRLA WILD-TYPE 
          78.67          238.29 
  FCRLA MUTATED FCRLA WILD-TYPE 
         11.605          19.890 
[1] "1.2 - 78.7 (11.6)"  "0.0 - 238.3 (19.9)"
[1] "hr=" "1.2"
D24V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FCRLA MUTATED         0        3        5         2         0          4
  FCRLA WILD-TYPE       4      120      127        45        66         66
                 vv
clus              STAGE IIIB STAGE IV
  FCRLA MUTATED            1        0
  FCRLA WILD-TYPE         10       25
D24V3, multiclass
            clus
vv           FCRLA MUTATED FCRLA WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               5             127
  STAGE IIA              2              45
  STAGE IIB              0              66
  STAGE IIIA             4              66
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FCRLA MUTATED     4   8   1   2
  FCRLA WILD-TYPE 151 253  42  16
D24V4, multiclass
    clus
vv   FCRLA MUTATED FCRLA WILD-TYPE
  T1             4             151
  T2             8             253
  T3             1              42
  T4             2              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
  FCRLA MUTATED    10   1     4
  FCRLA WILD-TYPE 297  88    68
D24V5, multiclass
       clus
vv      FCRLA MUTATED FCRLA WILD-TYPE
  N0               10             297
  N1                1              88
  N2+N3             4              68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                 cls
clus                0   1
  FCRLA MUTATED    11   0
  FCRLA WILD-TYPE 317  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED     11    0
  FCRLA WILD-TYPE  317   23
   clus
vv  FCRLA MUTATED FCRLA WILD-TYPE
  0            11             317
  1             0              23
[1] 2 2
[1] FALSE
D24V7, binary
                 cls
clus                0   1
  FCRLA MUTATED     8   7
  FCRLA WILD-TYPE 251 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      8    7
  FCRLA WILD-TYPE  251  214
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  FEMALE             8             251
  MALE               7             214
[1] 2 2
[1] FALSE
D24V8, binary
                 cls
clus                0   1
  FCRLA MUTATED     8   2
  FCRLA WILD-TYPE 325  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      8    2
  FCRLA WILD-TYPE  325   47
     clus
vv    FCRLA MUTATED FCRLA WILD-TYPE
  NO              8             325
  YES             2              47
[1] 2 2
[1] FALSE
D24V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FCRLA MUTATED                            0                                 3
  FCRLA WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FCRLA MUTATED                                                    9
  FCRLA WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FCRLA MUTATED                                            0
  FCRLA WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FCRLA MUTATED                                               1
  FCRLA WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  FCRLA MUTATED                                0
  FCRLA WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  FCRLA MUTATED                                    0
  FCRLA WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FCRLA MUTATED                              0                             1
  FCRLA WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FCRLA MUTATED                                               1
  FCRLA WILD-TYPE                                             4
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  FCRLA MUTATED                              0
  FCRLA WILD-TYPE                            9
D24V10, multiclass
                                                    clus
vv                                                   FCRLA MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  1
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   FCRLA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
D24V12, continuous
                 vv
clus               R0  R1  R2  RX
  FCRLA MUTATED     7   1   0   1
  FCRLA WILD-TYPE 303  10   4  24
D24V13, multiclass
    clus
vv   FCRLA MUTATED FCRLA WILD-TYPE
  R0             7             303
  R1             1              10
  R2             0               4
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FCRLA MUTATED                                  0     0
  FCRLA WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FCRLA MUTATED                           3    11
  FCRLA WILD-TYPE                        26   366
D24V14, multiclass
                                  clus
vv                                 FCRLA MUTATED FCRLA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    3              26
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, binary
                 cls
clus                0   1
  FCRLA MUTATED     0  13
  FCRLA WILD-TYPE   6 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      0   13
  FCRLA WILD-TYPE    6  336
                        clus
vv                       FCRLA MUTATED FCRLA WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            13             336
[1] 2 2
[1] FALSE

Clustering(25) Variable = ARID2 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    15   9
  ARID2 WILD-TYPE 287 146
  ARID2 MUTATED ARID2 WILD-TYPE 
             24             433 
  ARID2 MUTATED ARID2 WILD-TYPE 
              9             146 
$`ARID2 MUTATED`
TCGA-05-4396 TCGA-05-4397 TCGA-38-4631 TCGA-44-2656 TCGA-44-2657 TCGA-44-8120 
        9.96        24.03        11.64        46.98        44.42         8.55 
TCGA-50-5931 TCGA-50-6592 TCGA-55-7726 TCGA-55-7994 TCGA-55-8089 TCGA-55-8511 
       14.27        25.55         1.28        19.82         3.29         0.30 
TCGA-62-A46P TCGA-67-6217 TCGA-69-7974 TCGA-69-7978 TCGA-73-4658 TCGA-73-4675 
       19.53        13.87         6.05         4.41        52.60        30.31 
TCGA-78-7633 TCGA-86-6851 TCGA-91-6848 TCGA-91-6849 TCGA-93-8067 TCGA-MN-A4N4 
       50.24         5.88         7.36         1.15         6.12        38.63 

$`ARID2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        0.00        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        4.37        38.10        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       13.74        12.66         3.25        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.33        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        9.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1.32        23.18         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36         0.26         0.49        17.72         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01         6.90        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        4.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        10.55       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 
       10.19         2.60        13.71        12.23        27.68        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
       17.46        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        6.35        10.09        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ARID2 MUTATED ARID2 WILD-TYPE 
            0.3             0.0 
  ARID2 MUTATED ARID2 WILD-TYPE 
          52.60          238.29 
  ARID2 MUTATED ARID2 WILD-TYPE 
         12.755          19.890 
[1] "0.3 - 52.6 (12.8)"  "0.0 - 238.3 (19.9)"
[1] "hr=" "1.5"
D25V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARID2 MUTATED         0        3       11         2         3          4
  ARID2 WILD-TYPE       4      120      121        45        63         66
                 vv
clus              STAGE IIIB STAGE IV
  ARID2 MUTATED            1        0
  ARID2 WILD-TYPE         10       25
D25V3, multiclass
            clus
vv           ARID2 MUTATED ARID2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB              11             121
  STAGE IIA              2              45
  STAGE IIB              3              63
  STAGE IIIA             4              66
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARID2 MUTATED     4  17   2   1
  ARID2 WILD-TYPE 151 244  41  17
D25V4, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  T1             4             151
  T2            17             244
  T3             2              41
  T4             1              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
  ARID2 MUTATED    14   6     3
  ARID2 WILD-TYPE 293  83    69
D25V5, multiclass
       clus
vv      ARID2 MUTATED ARID2 WILD-TYPE
  N0               14             293
  N1                6              83
  N2+N3             3              69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                 cls
clus                0   1
  ARID2 MUTATED    16   0
  ARID2 WILD-TYPE 312  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     16    0
  ARID2 WILD-TYPE  312   23
   clus
vv  ARID2 MUTATED ARID2 WILD-TYPE
  0            16             312
  1             0              23
[1] 2 2
[1] FALSE
D25V7, binary
                 cls
clus                0   1
  ARID2 MUTATED    11  13
  ARID2 WILD-TYPE 248 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     11   13
  ARID2 WILD-TYPE  248  208
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE            11             248
  MALE              13             208
[1] 2 2
[1] FALSE
D25V8, binary
                 cls
clus                0   1
  ARID2 MUTATED    16   2
  ARID2 WILD-TYPE 317  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     16    2
  ARID2 WILD-TYPE  317   47
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             16             317
  YES             2              47
[1] 2 2
[1] FALSE
D25V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARID2 MUTATED                            0                                 7
  ARID2 WILD-TYPE                         18                                94
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARID2 MUTATED                                                   17
  ARID2 WILD-TYPE                                                278
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ARID2 MUTATED                                            0
  ARID2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ARID2 MUTATED                                               0
  ARID2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ARID2 MUTATED                                0
  ARID2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ARID2 MUTATED                                    0
  ARID2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ARID2 MUTATED                              0                             0
  ARID2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ARID2 MUTATED                                               0
  ARID2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ARID2 MUTATED                              0
  ARID2 WILD-TYPE                            9
D25V10, multiclass
                                                    clus
vv                                                   ARID2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ARID2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             278
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
D25V12, continuous
                 vv
clus               R0  R1  R2  RX
  ARID2 MUTATED    14   0   0   2
  ARID2 WILD-TYPE 296  11   4  23
D25V13, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  R0            14             296
  R1             0              11
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID2 MUTATED                                  0     1
  ARID2 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED                           2    19
  ARID2 WILD-TYPE                        27   358
D25V14, multiclass
                                  clus
vv                                 ARID2 MUTATED ARID2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       19             358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V15, binary
                 cls
clus                0   1
  ARID2 MUTATED     0  21
  ARID2 WILD-TYPE   6 328
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      0   21
  ARID2 WILD-TYPE    6  328
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            21             328
[1] 2 2
[1] FALSE

Clustering(26) Variable = APC MUTATION ANALYSIS
D26V1, survival
               sevent
clus2             0   1
  APC MUTATED    12   8
  APC WILD-TYPE 290 147
  APC MUTATED APC WILD-TYPE 
           20           437 
  APC MUTATED APC WILD-TYPE 
            8           147 
$`APC MUTATED`
TCGA-05-4382 TCGA-05-4397 TCGA-05-4402 TCGA-38-4631 TCGA-44-7661 TCGA-44-A4SS 
       19.96        24.03         8.02        11.64        12.03        13.64 
TCGA-49-4507 TCGA-49-6761 TCGA-50-5049 TCGA-50-5930 TCGA-50-8457 TCGA-55-5899 
        8.81        11.64        70.55         9.27        36.99         2.86 
TCGA-55-8510 TCGA-62-8395 TCGA-69-7978 TCGA-73-4659 TCGA-78-7153 TCGA-78-7220 
       17.72        39.98         4.41        23.38       119.51        26.53 
TCGA-78-8662 TCGA-91-6840 
      110.50        12.23 

$`APC WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
        9.96        47.05        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        44.42        38.10        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.08        11.54        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       17.16        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         8.09        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69         0.72        10.13         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94        35.21        23.05        48.62 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.26         0.49         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 
        0.92        15.81        20.19        19.99         4.57        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 
       17.16         2.01         6.90        52.60        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       50.33       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
      129.53        21.90        39.95        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        13.71        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29        41.82        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  APC MUTATED APC WILD-TYPE 
         2.86          0.00 
  APC MUTATED APC WILD-TYPE 
       119.51        238.29 
  APC MUTATED APC WILD-TYPE 
        15.68         19.82 
[1] "2.9 - 119.5 (15.7)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1"  
D26V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  APC MUTATED         0        5        6         0         3          5
  APC WILD-TYPE       4      118      126        47        63         65
               vv
clus            STAGE IIIB STAGE IV
  APC MUTATED            0        1
  APC WILD-TYPE         11       24
D26V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I              0             4
  STAGE IA             5           118
  STAGE IB             6           126
  STAGE IIA            0            47
  STAGE IIB            3            63
  STAGE IIIA           5            65
  STAGE IIIB           0            11
  STAGE IV             1            24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  APC MUTATED     5  13   2   0
  APC WILD-TYPE 150 248  41  18
D26V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           5           150
  T2          13           248
  T3           2            41
  T4           0            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
  APC MUTATED    11   4     4
  APC WILD-TYPE 296  85    68
D26V5, multiclass
       clus
vv      APC MUTATED APC WILD-TYPE
  N0             11           296
  N1              4            85
  N2+N3           4            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
               cls
clus              0   1
  APC MUTATED    16   1
  APC WILD-TYPE 312  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     16    1
  APC WILD-TYPE  312   22
   clus
vv  APC MUTATED APC WILD-TYPE
  0          16           312
  1           1            22
[1] 2 2
[1] FALSE
D26V7, binary
               cls
clus              0   1
  APC MUTATED    12   8
  APC WILD-TYPE 247 213
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     12    8
  APC WILD-TYPE  247  213
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          12           247
  MALE             8           213
[1] 2 2
[1] FALSE
D26V8, binary
               cls
clus              0   1
  APC MUTATED    13   4
  APC WILD-TYPE 320  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     13    4
  APC WILD-TYPE  320   45
     clus
vv    APC MUTATED APC WILD-TYPE
  NO           13           320
  YES           4            45
[1] 2 2
[1] FALSE
D26V9, continuous
[1] "Remove cluster labels:" "APC MUTATED"           
clus
  APC MUTATED APC WILD-TYPE 
            2           115 
   TCGA-35-4122    TCGA-35-4123    TCGA-35-5375    TCGA-44-3396    TCGA-44-3918 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-44-4112    TCGA-44-6144    TCGA-44-6147    TCGA-44-6775    TCGA-44-7660 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-44-A47F    TCGA-49-4486    TCGA-49-4494    TCGA-49-4505    TCGA-49-4506 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-49-4510    TCGA-49-6742    TCGA-49-6743    TCGA-49-6744    TCGA-53-7624 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-53-A4EZ    TCGA-55-7283    TCGA-55-7573    TCGA-55-7725    TCGA-55-7910 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-55-7914    TCGA-55-8089    TCGA-55-8096    TCGA-55-8205    TCGA-55-8208 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-55-8507    TCGA-55-8508    TCGA-55-8511    TCGA-55-8512    TCGA-55-8619 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-55-8620    TCGA-55-8621    TCGA-55-A48Z    TCGA-55-A490    TCGA-55-A491 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-55-A492    TCGA-55-A494    TCGA-62-8394    TCGA-62-8397    TCGA-62-8398 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-62-8399    TCGA-62-8402    TCGA-62-A46O    TCGA-62-A46P    TCGA-62-A46R 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-62-A46S    TCGA-62-A46U    TCGA-62-A46V    TCGA-62-A46Y    TCGA-62-A470 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-62-A471    TCGA-62-A472    TCGA-64-1677    TCGA-64-1681    TCGA-64-5775 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-64-5778    TCGA-69-7974    TCGA-69-8254    TCGA-71-6725    TCGA-71-8520 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-73-4662    TCGA-73-4666    TCGA-73-4668    TCGA-73-4670    TCGA-73-4676 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-73-4677    TCGA-73-7498    TCGA-73-7499    TCGA-75-5122    TCGA-83-5908 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-86-6562    TCGA-86-6851    TCGA-86-7701    TCGA-86-7711    TCGA-86-7713 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-86-7714    TCGA-86-7953    TCGA-86-7954    TCGA-86-7955    TCGA-86-8054 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-86-8055    TCGA-86-8056    TCGA-86-8073    TCGA-86-8074    TCGA-86-8075 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-86-8076    TCGA-86-8278    TCGA-86-8279    TCGA-86-8280    TCGA-86-8281 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-86-8358    TCGA-86-8359    TCGA-86-8668    TCGA-86-8669    TCGA-86-8671 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-86-A456    TCGA-86-A4JF    TCGA-86-A4P7    TCGA-91-6829    TCGA-91-6849 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-93-7347    TCGA-93-7348    TCGA-93-8067    TCGA-93-A4JN    TCGA-93-A4JO 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-95-7567    TCGA-99-7458    TCGA-MN-A4N1    TCGA-MN-A4N4    TCGA-MN-A4N5 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  APC MUTATED                            0                                 9
  APC WILD-TYPE                         18                                92
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  APC MUTATED                                                   11
  APC WILD-TYPE                                                284
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  APC MUTATED                                            0
  APC WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  APC MUTATED                                               0
  APC WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  APC MUTATED                                0
  APC WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  APC MUTATED                                    0                            0
  APC WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  APC MUTATED                               0
  APC WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  APC MUTATED                                               0
  APC WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  APC MUTATED                              0
  APC WILD-TYPE                            9
D26V10, multiclass
                                                    clus
vv                                                   APC MUTATED APC WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            9            92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          11           284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
D26V12, continuous
               vv
clus             R0  R1  R2  RX
  APC MUTATED    13   0   1   0
  APC WILD-TYPE 297  11   3  25
D26V13, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          13           297
  R1           0            11
  R2           1             3
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APC MUTATED                                  0     0
  APC WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  APC MUTATED                           1    15
  APC WILD-TYPE                        28   362
D26V14, multiclass
                                  clus
vv                                 APC MUTATED APC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                     15           362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V15, binary
               cls
clus              0   1
  APC MUTATED     0  14
  APC WILD-TYPE   6 335
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      0   14
  APC WILD-TYPE    6  335
                        clus
vv                       APC MUTATED APC WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          14           335
[1] 2 2
[1] FALSE

Clustering(27) Variable = ZEB1 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  ZEB1 MUTATED    23   8
  ZEB1 WILD-TYPE 279 147
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            31            426 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
             8            147 
$`ZEB1 MUTATED`
TCGA-05-4250 TCGA-05-4424 TCGA-35-4123 TCGA-44-2656 TCGA-44-7662 TCGA-44-7671 
        3.98        30.02         5.98        46.98         7.17        29.23 
TCGA-49-6743 TCGA-50-5049 TCGA-55-1592 TCGA-55-7281 TCGA-55-7283 TCGA-55-8616 
       53.29        70.55        23.05         0.59         1.15         1.58 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-A46V TCGA-64-5774 TCGA-64-5779 TCGA-69-7761 
       20.19        19.99        72.30        87.98        28.41         6.12 
TCGA-69-7973 TCGA-69-8254 TCGA-73-4666 TCGA-78-7146 TCGA-78-7162 TCGA-78-8640 
        7.56        13.45        26.30         5.69       104.19       232.18 
TCGA-86-8585 TCGA-86-A456 TCGA-93-A4JO TCGA-97-7937 TCGA-MN-A4N4 TCGA-MP-A4T2 
        1.15        29.46         1.08         5.95        38.63        37.35 
TCGA-NJ-A4YI 
        0.13 

$`ZEB1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        4.37        44.42        38.10        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 
       19.46        12.03        36.07        18.87        29.00        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
        8.81        29.46        29.75        55.89        16.04        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
       17.16        11.64        22.26        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       35.21        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7284 
       24.99        40.54       107.21        70.26         1.74         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64        17.62         0.49         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       19.59         0.92        15.81         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       54.35        67.96        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
       56.81        20.65        81.80        38.37         2.04        42.90 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       51.25        28.47        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64        13.87         6.64        22.68        13.61 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24        17.16         2.01         6.90        52.60        23.38 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       82.68        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
       39.09        50.33       163.10        27.16        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 
       32.09         5.88        64.90        22.92         9.57       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55        50.24        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP 
       19.82        22.45        17.46         6.12        23.61        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30         6.35        10.09        27.19         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       58.45        49.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ZEB1 MUTATED ZEB1 WILD-TYPE 
          0.13           0.00 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
        232.18         238.29 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
        20.190         19.745 
[1] "0.1 - 232.2 (20.2)" "0.0 - 238.3 (19.7)"
[1] "hr=" "1.7"
D27V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZEB1 MUTATED         0       11       10         1         1          7
  ZEB1 WILD-TYPE       4      112      122        46        65         63
                vv
clus             STAGE IIIB STAGE IV
  ZEB1 MUTATED            0        1
  ZEB1 WILD-TYPE         11       24
D27V3, multiclass
            clus
vv           ZEB1 MUTATED ZEB1 WILD-TYPE
  STAGE I               0              4
  STAGE IA             11            112
  STAGE IB             10            122
  STAGE IIA             1             46
  STAGE IIB             1             65
  STAGE IIIA            7             63
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZEB1 MUTATED    12  17   3   0
  ZEB1 WILD-TYPE 143 244  40  18
D27V4, multiclass
    clus
vv   ZEB1 MUTATED ZEB1 WILD-TYPE
  T1           12            143
  T2           17            244
  T3            3             40
  T4            0             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
  ZEB1 MUTATED    23   2     6
  ZEB1 WILD-TYPE 284  87    66
D27V5, multiclass
       clus
vv      ZEB1 MUTATED ZEB1 WILD-TYPE
  N0              23            284
  N1               2             87
  N2+N3            6             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                cls
clus               0   1
  ZEB1 MUTATED    22   1
  ZEB1 WILD-TYPE 306  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED     22    1
  ZEB1 WILD-TYPE  306   22
   clus
vv  ZEB1 MUTATED ZEB1 WILD-TYPE
  0           22            306
  1            1             22
[1] 2 2
[1] FALSE
D27V7, binary
                cls
clus               0   1
  ZEB1 MUTATED    12  20
  ZEB1 WILD-TYPE 247 201
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED     12   20
  ZEB1 WILD-TYPE  247  201
        clus
vv       ZEB1 MUTATED ZEB1 WILD-TYPE
  FEMALE           12            247
  MALE             20            201
[1] 2 2
[1] FALSE
D27V8, binary
                cls
clus               0   1
  ZEB1 MUTATED    21   4
  ZEB1 WILD-TYPE 312  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED     21    4
  ZEB1 WILD-TYPE  312   45
     clus
vv    ZEB1 MUTATED ZEB1 WILD-TYPE
  NO            21            312
  YES            4             45
[1] 2 2
[1] FALSE
D27V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZEB1 MUTATED                            2                                 8
  ZEB1 WILD-TYPE                         16                                93
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZEB1 MUTATED                                                   16
  ZEB1 WILD-TYPE                                                279
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZEB1 MUTATED                                            0
  ZEB1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZEB1 MUTATED                                               1
  ZEB1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  ZEB1 MUTATED                                1
  ZEB1 WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  ZEB1 MUTATED                                    1
  ZEB1 WILD-TYPE                                  2
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZEB1 MUTATED                              0                             2
  ZEB1 WILD-TYPE                            2                            20
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZEB1 MUTATED                                               1
  ZEB1 WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  ZEB1 MUTATED                              0
  ZEB1 WILD-TYPE                            9
D27V10, multiclass
                                                    clus
vv                                                   ZEB1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           16
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            1
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   ZEB1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              93
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              2
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
D27V12, continuous
                vv
clus              R0  R1  R2  RX
  ZEB1 MUTATED    18   1   1   1
  ZEB1 WILD-TYPE 292  10   3  24
D27V13, multiclass
    clus
vv   ZEB1 MUTATED ZEB1 WILD-TYPE
  R0           18            292
  R1            1             10
  R2            1              3
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZEB1 MUTATED                                  0     1
  ZEB1 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZEB1 MUTATED                           1    26
  ZEB1 WILD-TYPE                        28   351
D27V14, multiclass
                                  clus
vv                                 ZEB1 MUTATED ZEB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              6
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      26            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, binary
                cls
clus               0   1
  ZEB1 MUTATED     0  23
  ZEB1 WILD-TYPE   6 326
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED      0   23
  ZEB1 WILD-TYPE    6  326
                        clus
vv                       ZEB1 MUTATED ZEB1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           23            326
[1] 2 2
[1] FALSE

Clustering(28) Variable = SIP1 MUTATION ANALYSIS
D28V1, survival
                sevent
clus2              0   1
  SIP1 MUTATED     2   2
  SIP1 WILD-TYPE 300 153
  SIP1 MUTATED SIP1 WILD-TYPE 
             4            453 
  SIP1 MUTATED SIP1 WILD-TYPE 
             2            153 
$`SIP1 MUTATED`
TCGA-44-3919 TCGA-55-1592 TCGA-55-1595 TCGA-95-7567 
       33.73        23.05        48.62        18.67 

$`SIP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 
       38.10        42.77        37.15        38.24        34.06        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
       17.29        41.82        16.54         2.86        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  SIP1 MUTATED SIP1 WILD-TYPE 
         18.67           0.00 
  SIP1 MUTATED SIP1 WILD-TYPE 
         48.62         238.29 
  SIP1 MUTATED SIP1 WILD-TYPE 
         28.39          19.76 
[1] "18.7 - 48.6 (28.4)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.2"
D28V2, continuous
[1] "Remove cluster labels:" "SIP1 MUTATED"          
clus
  SIP1 MUTATED SIP1 WILD-TYPE 
             2            447 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4402 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4405     TCGA-05-4410     TCGA-05-4415 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4418     TCGA-05-4420     TCGA-05-4422 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4424     TCGA-05-4425     TCGA-05-4426     TCGA-05-4427 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-4434 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5425     TCGA-05-5428 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-5429     TCGA-05-5715     TCGA-35-4122     TCGA-35-4123 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-4627 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-38-4628     TCGA-38-4629     TCGA-38-4630     TCGA-38-4631 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-38-4632     TCGA-38-6178     TCGA-38-7271     TCGA-38-A44F 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-2656     TCGA-44-2657     TCGA-44-2661     TCGA-44-2665 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3398     TCGA-44-3918     TCGA-44-4112 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-5643     TCGA-44-5644     TCGA-44-5645     TCGA-44-6144 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-6145     TCGA-44-6146     TCGA-44-6147     TCGA-44-6148 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-6774     TCGA-44-6775     TCGA-44-6776     TCGA-44-6777 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-6778     TCGA-44-6779     TCGA-44-7659     TCGA-44-7660 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-7661     TCGA-44-7662     TCGA-44-7667     TCGA-44-7669 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-7670     TCGA-44-7671     TCGA-44-7672     TCGA-44-8117 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-8119     TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4487     TCGA-49-4488 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4490     TCGA-49-4494     TCGA-49-4501     TCGA-49-4505 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4506     TCGA-49-4507     TCGA-49-4510     TCGA-49-4512 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4514     TCGA-49-6742     TCGA-49-6743     TCGA-49-6744 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-6745     TCGA-49-6761     TCGA-49-6767     TCGA-50-5044 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-5045     TCGA-50-5049     TCGA-50-5051     TCGA-50-5055 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-5066     TCGA-50-5068     TCGA-50-5072     TCGA-50-5930 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-5931     TCGA-50-5932     TCGA-50-5933     TCGA-50-5935 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-5936     TCGA-50-5939     TCGA-50-5941     TCGA-50-5942 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-5944     TCGA-50-5946     TCGA-50-6590     TCGA-50-6591 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-6592     TCGA-50-6593     TCGA-50-6594     TCGA-50-6595 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-6597     TCGA-50-6673     TCGA-50-7109     TCGA-50-8457 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-8459     TCGA-50-8460     TCGA-53-7624     TCGA-53-7626 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-53-7813     TCGA-53-A4EZ     TCGA-55-6642     TCGA-55-6968 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-6969     TCGA-55-6970     TCGA-55-6971     TCGA-55-6972 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-6979     TCGA-55-6981     TCGA-55-6985     TCGA-55-6987 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7227     TCGA-55-7281     TCGA-55-7283     TCGA-55-7284 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7570     TCGA-55-7573     TCGA-55-7574     TCGA-55-7576 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7724     TCGA-55-7725     TCGA-55-7726     TCGA-55-7727 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7728     TCGA-55-7815     TCGA-55-7816     TCGA-55-7903 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7907     TCGA-55-7910     TCGA-55-7911     TCGA-55-7914 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7994     TCGA-55-7995     TCGA-55-8085     TCGA-55-8087 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8090     TCGA-55-8091     TCGA-55-8092 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8096     TCGA-55-8097     TCGA-55-8203 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8204     TCGA-55-8205     TCGA-55-8206     TCGA-55-8207 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8505     TCGA-55-8506     TCGA-55-8507     TCGA-55-8508 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8510     TCGA-55-8511     TCGA-55-8512     TCGA-55-8513 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8614     TCGA-55-8615     TCGA-55-8616 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-A4DG     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1676     TCGA-64-1677     TCGA-64-1679 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-64-1681     TCGA-64-5774     TCGA-64-5775     TCGA-64-5778 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-64-5779     TCGA-64-5781     TCGA-64-5815     TCGA-67-3771 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-67-3772     TCGA-67-3773     TCGA-67-4679     TCGA-67-6215 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-67-6216     TCGA-67-6217     TCGA-69-7760     TCGA-69-7761 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-69-7763     TCGA-69-7764     TCGA-69-7765     TCGA-69-7973 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-7978     TCGA-69-7979     TCGA-69-7980 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-69-8253     TCGA-69-8254     TCGA-69-8255     TCGA-69-A59K 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4658     TCGA-73-4659 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-4677     TCGA-73-7498 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-7499     TCGA-78-7143     TCGA-78-7145     TCGA-78-7146 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7147     TCGA-78-7148     TCGA-78-7149     TCGA-78-7150 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7152     TCGA-78-7153     TCGA-78-7154     TCGA-78-7155 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7156     TCGA-78-7158     TCGA-78-7159     TCGA-78-7160 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7161     TCGA-78-7162     TCGA-78-7163     TCGA-78-7166 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7167     TCGA-78-7220     TCGA-78-7535     TCGA-78-7536 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7537     TCGA-78-7539     TCGA-78-7540     TCGA-78-7542 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-83-5908     TCGA-86-6562 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-6851     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7953     TCGA-86-7954     TCGA-86-7955 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8280     TCGA-86-8281     TCGA-86-8358 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8585     TCGA-86-8668     TCGA-86-8669 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8671     TCGA-86-8672     TCGA-86-8673     TCGA-86-8674 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-86-A4P8 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-6828     TCGA-91-6829     TCGA-91-6830     TCGA-91-6831 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-6835     TCGA-91-6836     TCGA-91-6840     TCGA-91-6847 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-6848     TCGA-91-6849     TCGA-91-7771     TCGA-91-8496 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-8497     TCGA-91-8499     TCGA-91-A4BC     TCGA-91-A4BD 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JP     TCGA-93-A4JQ     TCGA-95-7039 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-95-7043     TCGA-95-7562     TCGA-95-7944     TCGA-95-7947 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-95-7948     TCGA-95-8039     TCGA-95-8494     TCGA-95-A4VK 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546     TCGA-97-7547 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-7552     TCGA-97-7553     TCGA-97-7554     TCGA-97-7937 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-7938     TCGA-97-7941     TCGA-97-8171     TCGA-97-8172 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-8174     TCGA-97-8175     TCGA-97-8176     TCGA-97-8177 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-8179     TCGA-97-8547     TCGA-97-8552     TCGA-97-A4LX 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2     TCGA-97-A4M3 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-A4M5     TCGA-97-A4M6     TCGA-97-A4M7     TCGA-99-7458 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-99-8033 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-J2-8192     TCGA-J2-8194     TCGA-J2-A4AD     TCGA-J2-A4AE 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6     TCGA-L9-A443 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY     TCGA-MP-A4T2 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7     TCGA-MP-A4T8 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TD 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YF     TCGA-NJ-A4YG 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-NJ-A4YI     TCGA-NJ-A4YP     TCGA-NJ-A4YQ     TCGA-NJ-A55A 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-NJ-A55O     TCGA-NJ-A55R     TCGA-O1-A52J 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SIP1 MUTATED         0        3        0         0         1          0
  SIP1 WILD-TYPE       4      120      132        47        65         70
                vv
clus             STAGE IIIB STAGE IV
  SIP1 MUTATED            0        0
  SIP1 WILD-TYPE         11       25
D28V3, multiclass
            clus
vv           SIP1 MUTATED SIP1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            120
  STAGE IB              0            132
  STAGE IIA             0             47
  STAGE IIB             1             65
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SIP1 MUTATED     2   2   0   0
  SIP1 WILD-TYPE 153 259  43  18
D28V4, multiclass
    clus
vv   SIP1 MUTATED SIP1 WILD-TYPE
  T1            2            153
  T2            2            259
  T3            0             43
  T4            0             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
  SIP1 MUTATED     3   1     0
  SIP1 WILD-TYPE 304  88    72
D28V5, multiclass
       clus
vv      SIP1 MUTATED SIP1 WILD-TYPE
  N0               3            304
  N1               1             88
  N2+N3            0             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                cls
clus               0   1
  SIP1 MUTATED     4   0
  SIP1 WILD-TYPE 324  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIP1 MUTATED      4    0
  SIP1 WILD-TYPE  324   23
   clus
vv  SIP1 MUTATED SIP1 WILD-TYPE
  0            4            324
  1            0             23
[1] 2 2
[1] FALSE
D28V7, binary
                cls
clus               0   1
  SIP1 MUTATED     2   2
  SIP1 WILD-TYPE 257 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIP1 MUTATED      2    2
  SIP1 WILD-TYPE  257  219
        clus
vv       SIP1 MUTATED SIP1 WILD-TYPE
  FEMALE            2            257
  MALE              2            219
[1] 2 2
[1] FALSE
D28V8, binary
                cls
clus               0   1
  SIP1 MUTATED     4   0
  SIP1 WILD-TYPE 329  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIP1 MUTATED      4    0
  SIP1 WILD-TYPE  329   49
     clus
vv    SIP1 MUTATED SIP1 WILD-TYPE
  NO             4            329
  YES            0             49
[1] 2 2
[1] FALSE
D28V9, continuous
[1] "Remove cluster labels:" "SIP1 MUTATED"          
clus
  SIP1 MUTATED SIP1 WILD-TYPE 
             1            116 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-44-3396 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-6144     TCGA-44-6147 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-44-A47F     TCGA-49-4486 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4494     TCGA-49-4505     TCGA-49-4506     TCGA-49-4510 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-6742     TCGA-49-6743     TCGA-49-6744     TCGA-53-7624 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-53-A4EZ     TCGA-55-7283     TCGA-55-7573     TCGA-55-7725 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7914     TCGA-55-8089     TCGA-55-8096 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8208     TCGA-55-8507     TCGA-55-8508 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8619     TCGA-55-8620 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8621     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-69-7974     TCGA-69-8254 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4659     TCGA-73-4662 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-4666     TCGA-73-4668     TCGA-73-4670     TCGA-73-4676 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-4677     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6562     TCGA-86-6851     TCGA-86-7701 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-7711     TCGA-86-7713     TCGA-86-7714     TCGA-86-7953 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8054     TCGA-86-8055 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8075 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8280 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8281     TCGA-86-8358     TCGA-86-8359     TCGA-86-8668 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8671     TCGA-86-A456     TCGA-86-A4JF 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-91-6829     TCGA-91-6849     TCGA-93-7347 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-99-7458     TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SIP1 MUTATED                            0                                 1
  SIP1 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SIP1 MUTATED                                                    2
  SIP1 WILD-TYPE                                                293
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SIP1 MUTATED                                            0
  SIP1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SIP1 MUTATED                                               0
  SIP1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SIP1 MUTATED                                1
  SIP1 WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SIP1 MUTATED                                    0
  SIP1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SIP1 MUTATED                              0                             0
  SIP1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SIP1 MUTATED                                               0
  SIP1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SIP1 MUTATED                              0
  SIP1 WILD-TYPE                            9
D28V10, multiclass
                                                    clus
vv                                                   SIP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SIP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
D28V12, continuous
                vv
clus              R0  R1  R2  RX
  SIP1 MUTATED     2   0   0   0
  SIP1 WILD-TYPE 308  11   4  25
D28V13, multiclass
[1] "Remove cluster labels:" "SIP1 MUTATED"          
clus
  SIP1 MUTATED SIP1 WILD-TYPE 
             2            348 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4402 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4405     TCGA-05-4410     TCGA-05-4415 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4418     TCGA-05-4420     TCGA-05-4422 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4424     TCGA-05-4425     TCGA-05-4426     TCGA-05-4427 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-4434 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5425     TCGA-05-5428 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-5429     TCGA-05-5715     TCGA-35-4122     TCGA-35-4123 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-4627 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-38-4628     TCGA-38-4629     TCGA-38-4630     TCGA-38-4631 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-38-4632     TCGA-38-6178     TCGA-38-7271     TCGA-38-A44F 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-2657     TCGA-44-2661     TCGA-44-2665     TCGA-44-3396 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-4112     TCGA-44-6144 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6775     TCGA-44-A479     TCGA-44-A47A 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47G     TCGA-44-A4SU     TCGA-49-4486 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4487     TCGA-49-4488     TCGA-49-4494     TCGA-49-4501 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4507     TCGA-49-4510 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4512     TCGA-49-4514     TCGA-49-6742     TCGA-49-6744 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-6761     TCGA-49-6767     TCGA-50-5051     TCGA-50-5055 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-5066     TCGA-50-5931     TCGA-50-5942     TCGA-50-5944 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-6593     TCGA-50-6597     TCGA-50-6673     TCGA-50-8460 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-A4EZ     TCGA-55-5899 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-6642     TCGA-55-6970     TCGA-55-6971     TCGA-55-6972 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-6980     TCGA-55-6981     TCGA-55-6983     TCGA-55-6985 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7281     TCGA-55-7284     TCGA-55-7570     TCGA-55-7574 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7576     TCGA-55-7724     TCGA-55-7725     TCGA-55-7726 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7727     TCGA-55-7728     TCGA-55-7815     TCGA-55-7903 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7907     TCGA-55-7910     TCGA-55-7911     TCGA-55-7914 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7994     TCGA-55-7995     TCGA-55-8085     TCGA-55-8087 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8090     TCGA-55-8091     TCGA-55-8092 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8097     TCGA-55-8203     TCGA-55-8204 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8206     TCGA-55-8207     TCGA-55-8208 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8505 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8508     TCGA-55-8510 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8513     TCGA-55-8514 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8614     TCGA-55-8615     TCGA-55-8616     TCGA-55-8619 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF     TCGA-55-A4DG 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-8394     TCGA-62-8395     TCGA-62-8397     TCGA-62-8398 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-64-1676     TCGA-64-1677     TCGA-64-1679     TCGA-64-1681 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-64-5774     TCGA-64-5775     TCGA-64-5778     TCGA-64-5779 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-64-5781     TCGA-64-5815     TCGA-67-3771     TCGA-67-3773 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-67-4679     TCGA-67-6215     TCGA-67-6216     TCGA-67-6217 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4658     TCGA-73-4659 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-4677     TCGA-73-7498 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-7499     TCGA-75-5122     TCGA-75-5125     TCGA-75-5126 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-75-5146     TCGA-75-5147     TCGA-75-6203     TCGA-75-6205 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-75-6206     TCGA-75-6207     TCGA-75-6211     TCGA-75-6212 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-75-6214     TCGA-75-7025     TCGA-75-7027     TCGA-75-7030 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-75-7031     TCGA-78-7143     TCGA-78-7145     TCGA-78-7146 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7147     TCGA-78-7148     TCGA-78-7149     TCGA-78-7150 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7152     TCGA-78-7153     TCGA-78-7154     TCGA-78-7155 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7156     TCGA-78-7158     TCGA-78-7159     TCGA-78-7160 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7161     TCGA-78-7162     TCGA-78-7163     TCGA-78-7166 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7167     TCGA-78-7220     TCGA-78-7535     TCGA-78-7536 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7537     TCGA-78-7539     TCGA-78-7540     TCGA-78-7542 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-80-5611     TCGA-83-5908     TCGA-86-6562     TCGA-86-7701 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-7711     TCGA-86-7713     TCGA-86-7714     TCGA-86-7953 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8054     TCGA-86-8055 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8075 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8280 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8585     TCGA-86-8668 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8671     TCGA-86-8672     TCGA-86-8673 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-6828     TCGA-91-6829     TCGA-91-6835     TCGA-91-6840 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-A4BD     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JP     TCGA-93-A4JQ 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-95-8039     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-97-7546 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-7554     TCGA-97-7938     TCGA-97-7941     TCGA-97-8176 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M7     TCGA-99-7458     TCGA-99-8025 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-99-8028     TCGA-99-8032     TCGA-99-8033     TCGA-J2-A4AD 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-J2-A4AE     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4T8     TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4TD     TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YQ 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIP1 MUTATED                                  0     1
  SIP1 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SIP1 MUTATED                           0     3
  SIP1 WILD-TYPE                        29   374
D28V14, multiclass
                                  clus
vv                                 SIP1 MUTATED SIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              6
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       3            374
[1] 4 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
  SIP1 MUTATED     0   4
  SIP1 WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIP1 MUTATED      0    4
  SIP1 WILD-TYPE    6  345
                        clus
vv                       SIP1 MUTATED SIP1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            345
[1] 2 2
[1] FALSE

Clustering(29) Variable = SLC4A3 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  SLC4A3 MUTATED    11   7
  SLC4A3 WILD-TYPE 291 148
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              18              439 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               7              148 
$`SLC4A3 MUTATED`
TCGA-44-2656 TCGA-44-5644 TCGA-49-4488 TCGA-50-5066 TCGA-50-5946 TCGA-55-8205 
       46.98        28.37        28.57        31.04        22.55         1.08 
TCGA-62-A46R TCGA-64-5778 TCGA-64-5781 TCGA-69-7978 TCGA-69-7980 TCGA-78-7156 
       56.71        42.90        51.25         4.41        12.56        32.09 
TCGA-78-7536 TCGA-91-6840 TCGA-95-7043 TCGA-95-7567 TCGA-MP-A4SY TCGA-MP-A4TA 
        8.02        12.23        16.54        18.67        49.35        31.23 

$`SLC4A3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        76.21        28.11        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94        35.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 
        0.13        23.64        15.65        17.98         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       87.98         2.04        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        2.93        14.01        13.45         4.24        17.16         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        6.90        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
       21.90        39.95       119.51        19.50        38.50         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53        31.20        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        13.71        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
       19.00        17.29        41.82         2.86        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
            1.08             0.00 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
           56.71           238.29 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
           28.47            19.73 
[1] "1.1 - 56.7 (28.5)"  "0.0 - 238.3 (19.7)"
[1] "hr=" "1"  
D29V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC4A3 MUTATED         1        5        6         0         4          1
  SLC4A3 WILD-TYPE       3      118      126        47        62         69
                  vv
clus               STAGE IIIB STAGE IV
  SLC4A3 MUTATED            0        1
  SLC4A3 WILD-TYPE         11       24
D29V3, multiclass
            clus
vv           SLC4A3 MUTATED SLC4A3 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                5              118
  STAGE IB                6              126
  STAGE IIA               0               47
  STAGE IIB               4               62
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC4A3 MUTATED     6  11   0   1
  SLC4A3 WILD-TYPE 149 250  43  17
D29V4, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  T1              6              149
  T2             11              250
  T3              0               43
  T4              1               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
  SLC4A3 MUTATED    13   4     1
  SLC4A3 WILD-TYPE 294  85    71
D29V5, multiclass
       clus
vv      SLC4A3 MUTATED SLC4A3 WILD-TYPE
  N0                13              294
  N1                 4               85
  N2+N3              1               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED    12   1
  SLC4A3 WILD-TYPE 316  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED     12    1
  SLC4A3 WILD-TYPE  316   22
   clus
vv  SLC4A3 MUTATED SLC4A3 WILD-TYPE
  0             12              316
  1              1               22
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED     9   9
  SLC4A3 WILD-TYPE 250 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      9    9
  SLC4A3 WILD-TYPE  250  212
        clus
vv       SLC4A3 MUTATED SLC4A3 WILD-TYPE
  FEMALE              9              250
  MALE                9              212
[1] 2 2
[1] FALSE
D29V8, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED    15   1
  SLC4A3 WILD-TYPE 318  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED     15    1
  SLC4A3 WILD-TYPE  318   48
     clus
vv    SLC4A3 MUTATED SLC4A3 WILD-TYPE
  NO              15              318
  YES              1               48
[1] 2 2
[1] FALSE
D29V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC4A3 MUTATED                            0                                 8
  SLC4A3 WILD-TYPE                         18                                93
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC4A3 MUTATED                                                    9
  SLC4A3 WILD-TYPE                                                286
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLC4A3 MUTATED                                            0
  SLC4A3 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLC4A3 MUTATED                                               1
  SLC4A3 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  SLC4A3 MUTATED                                0
  SLC4A3 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  SLC4A3 MUTATED                                    0
  SLC4A3 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLC4A3 MUTATED                              0                             0
  SLC4A3 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLC4A3 MUTATED                                               0
  SLC4A3 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  SLC4A3 MUTATED                              0
  SLC4A3 WILD-TYPE                            9
D29V10, multiclass
                                                    clus
vv                                                   SLC4A3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   SLC4A3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                93
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
D29V12, continuous
                  vv
clus                R0  R1  R2  RX
  SLC4A3 MUTATED    11   0   0   0
  SLC4A3 WILD-TYPE 299  11   4  25
D29V13, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  R0             11              299
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC4A3 MUTATED                                  0     0
  SLC4A3 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC4A3 MUTATED                           1    17
  SLC4A3 WILD-TYPE                        28   360
D29V14, multiclass
                                  clus
vv                                 SLC4A3 MUTATED SLC4A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        17              360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED     0  15
  SLC4A3 WILD-TYPE   6 334
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      0   15
  SLC4A3 WILD-TYPE    6  334
                        clus
vv                       SLC4A3 MUTATED SLC4A3 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             15              334
[1] 2 2
[1] FALSE

Clustering(30) Variable = STK19 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  STK19 MUTATED     3   2
  STK19 WILD-TYPE 299 153
  STK19 MUTATED STK19 WILD-TYPE 
              5             452 
  STK19 MUTATED STK19 WILD-TYPE 
              2             153 
$`STK19 MUTATED`
TCGA-55-8506 TCGA-62-A46Y TCGA-69-7979 TCGA-86-8671 TCGA-MP-A4TF 
        0.36        13.61         2.93        27.58        11.05 

$`STK19 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.33        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94        35.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 
       56.71        54.35        67.96        72.30        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  STK19 MUTATED STK19 WILD-TYPE 
           0.36            0.00 
  STK19 MUTATED STK19 WILD-TYPE 
          27.58          238.29 
  STK19 MUTATED STK19 WILD-TYPE 
          11.05           19.82 
[1] "0.4 - 27.6 (11.1)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "3.2"
D30V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  STK19 MUTATED         0        0        1         1         2          1
  STK19 WILD-TYPE       4      123      131        46        64         69
                 vv
clus              STAGE IIIB STAGE IV
  STK19 MUTATED            0        0
  STK19 WILD-TYPE         11       25
D30V3, multiclass
            clus
vv           STK19 MUTATED STK19 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               1             131
  STAGE IIA              1              46
  STAGE IIB              2              64
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK19 MUTATED     0   4   1   0
  STK19 WILD-TYPE 155 257  42  18
D30V4, multiclass
    clus
vv   STK19 MUTATED STK19 WILD-TYPE
  T1             0             155
  T2             4             257
  T3             1              42
  T4             0              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
  STK19 MUTATED     3   1     1
  STK19 WILD-TYPE 304  88    71
D30V5, multiclass
       clus
vv      STK19 MUTATED STK19 WILD-TYPE
  N0                3             304
  N1                1              88
  N2+N3             1              71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                 cls
clus                0   1
  STK19 MUTATED     3   0
  STK19 WILD-TYPE 325  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      3    0
  STK19 WILD-TYPE  325   23
   clus
vv  STK19 MUTATED STK19 WILD-TYPE
  0             3             325
  1             0              23
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus                0   1
  STK19 MUTATED     5   0
  STK19 WILD-TYPE 254 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      5    0
  STK19 WILD-TYPE  254  221
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  FEMALE             5             254
  MALE               0             221
[1] 2 2
[1] FALSE
D30V8, binary
                 cls
clus                0   1
  STK19 MUTATED     2   1
  STK19 WILD-TYPE 331  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      2    1
  STK19 WILD-TYPE  331   48
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              2             331
  YES             1              48
[1] 2 2
[1] FALSE
D30V9, continuous
[1] "Remove cluster labels:" "STK19 MUTATED"         
clus
  STK19 MUTATED STK19 WILD-TYPE 
              2             115 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-44-3396 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-6144      TCGA-44-6147 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-44-A47F      TCGA-49-4486 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-4494      TCGA-49-4505      TCGA-49-4506      TCGA-49-4510 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-6742      TCGA-49-6743      TCGA-49-6744      TCGA-53-7624 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-7283      TCGA-55-7573      TCGA-55-7725 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7914      TCGA-55-8089      TCGA-55-8096 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8208      TCGA-55-8507      TCGA-55-8508 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8511      TCGA-55-8512      TCGA-55-8619      TCGA-55-8620 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8621      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A470      TCGA-62-A471 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5775 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4676      TCGA-73-4677 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-6562      TCGA-86-6851      TCGA-86-7701      TCGA-86-7711 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7953      TCGA-86-7954 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-7955      TCGA-86-8054      TCGA-86-8055      TCGA-86-8056 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8073      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8280      TCGA-86-8281 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-91-6849      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567      TCGA-99-7458 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STK19 MUTATED                            1                                 1
  STK19 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STK19 MUTATED                                                    2
  STK19 WILD-TYPE                                                293
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STK19 MUTATED                                            0
  STK19 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STK19 MUTATED                                               0
  STK19 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  STK19 MUTATED                                0
  STK19 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  STK19 MUTATED                                    0
  STK19 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STK19 MUTATED                              0                             1
  STK19 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STK19 MUTATED                                               0
  STK19 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  STK19 MUTATED                              0
  STK19 WILD-TYPE                            9
D30V10, multiclass
                                                    clus
vv                                                   STK19 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   STK19 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
[1] "Remove cluster labels:" "STK19 MUTATED"         
clus
  STK19 MUTATED STK19 WILD-TYPE 
              2             331 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4382 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4384      TCGA-05-4389      TCGA-05-4390      TCGA-05-4396 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4397      TCGA-05-4398      TCGA-05-4405      TCGA-05-4410 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4415      TCGA-05-4417      TCGA-05-4418      TCGA-05-4420 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4422      TCGA-05-4424      TCGA-05-4425      TCGA-05-4426 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4430      TCGA-05-4432      TCGA-05-4433 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4434      TCGA-05-5420      TCGA-05-5423      TCGA-05-5425 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-5428      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-38-4625      TCGA-38-4626      TCGA-38-4629      TCGA-38-4631 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-38-4632      TCGA-38-7271      TCGA-38-A44F      TCGA-44-2656 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-2657      TCGA-44-3396      TCGA-44-3398      TCGA-44-3918 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-4112      TCGA-44-5643      TCGA-44-5644      TCGA-44-5645 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-6144      TCGA-44-6145      TCGA-44-6146      TCGA-44-6148 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-6774      TCGA-44-6775      TCGA-44-6776      TCGA-44-6777 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-6778      TCGA-44-6779      TCGA-44-7659      TCGA-44-7660 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-7661      TCGA-44-7662      TCGA-44-7667      TCGA-44-7669 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-7670      TCGA-44-7672      TCGA-44-8117      TCGA-44-8119 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS      TCGA-44-A4SU 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-4486      TCGA-49-4487      TCGA-49-4490      TCGA-49-4494 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4507      TCGA-49-4510 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-4514      TCGA-49-6742      TCGA-49-6743      TCGA-49-6744 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-6745      TCGA-49-6761      TCGA-49-6767      TCGA-50-5051 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-50-5072      TCGA-50-5931      TCGA-50-5939      TCGA-50-5941 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-50-5942      TCGA-50-6590      TCGA-50-7109      TCGA-50-8457 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-50-8459      TCGA-53-7624      TCGA-53-7626      TCGA-53-7813 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-6543      TCGA-55-6971      TCGA-55-6983 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-6985      TCGA-55-7281      TCGA-55-7283      TCGA-55-7574 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7724      TCGA-55-7725      TCGA-55-7726      TCGA-55-7728 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7903      TCGA-55-7907      TCGA-55-7910      TCGA-55-7911 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-7994      TCGA-55-7995      TCGA-55-8089 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8094      TCGA-55-8096      TCGA-55-8097 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8203      TCGA-55-8205      TCGA-55-8208      TCGA-55-8299 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8301      TCGA-55-8302      TCGA-55-8507      TCGA-55-8511 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8514      TCGA-55-8614      TCGA-55-8615 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X      TCGA-55-A48Y 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-A493      TCGA-55-A494      TCGA-55-A4DF      TCGA-55-A4DG 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-A46O      TCGA-62-A46P 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A470      TCGA-62-A471 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1676      TCGA-64-1677      TCGA-64-1679 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-64-5774      TCGA-64-5775      TCGA-64-5778      TCGA-64-5779 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-64-5781      TCGA-64-5815      TCGA-69-7761      TCGA-69-7763 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-69-7764      TCGA-69-7973      TCGA-69-7974      TCGA-69-7978 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-69-7980      TCGA-69-8253      TCGA-69-8254      TCGA-69-8255 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-69-A59K      TCGA-73-4658      TCGA-73-4659      TCGA-73-4662 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-4666      TCGA-73-4668      TCGA-73-4670      TCGA-73-4675 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-4676      TCGA-73-7498      TCGA-75-5122      TCGA-75-5125 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-75-5126      TCGA-75-6203      TCGA-75-6206      TCGA-75-6207 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-75-6211      TCGA-75-6214      TCGA-75-7027      TCGA-75-7031 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7145      TCGA-78-7146      TCGA-78-7147      TCGA-78-7148 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7149      TCGA-78-7150      TCGA-78-7152      TCGA-78-7153 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7154      TCGA-78-7155      TCGA-78-7156      TCGA-78-7158 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7159      TCGA-78-7160      TCGA-78-7161      TCGA-78-7162 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7163      TCGA-78-7166      TCGA-78-7167      TCGA-78-7220 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7535      TCGA-78-7536      TCGA-78-7537      TCGA-78-7539 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-80-5608      TCGA-80-5611      TCGA-83-5908      TCGA-86-6851 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7714      TCGA-86-7954 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8054      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8669      TCGA-86-8673      TCGA-86-8674      TCGA-91-6829 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-91-6830      TCGA-91-6835      TCGA-91-6836      TCGA-91-6840 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-91-6849      TCGA-91-7771      TCGA-91-8499      TCGA-91-A4BC 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-93-A4JO      TCGA-95-7039      TCGA-95-7043      TCGA-95-7562 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-95-7944      TCGA-95-7947      TCGA-95-7948      TCGA-95-A4VK 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-95-A4VN      TCGA-95-A4VP      TCGA-97-7546      TCGA-97-7547 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-7552      TCGA-97-7553      TCGA-97-7554      TCGA-97-7937 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-7938      TCGA-97-7941      TCGA-97-8171      TCGA-97-8172 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-8174      TCGA-97-8176      TCGA-97-8179      TCGA-97-A4LX 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M2      TCGA-97-A4M3 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-A4M5      TCGA-97-A4M7      TCGA-99-7458      TCGA-99-8025 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-99-8028      TCGA-99-8032      TCGA-J2-8194      TCGA-J2-A4AD 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6      TCGA-L9-A443 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-L9-A444      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4T8      TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4TD      TCGA-MP-A4TE      TCGA-MP-A4TH      TCGA-MP-A4TI 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YF      TCGA-NJ-A4YG 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-NJ-A4YI      TCGA-NJ-A4YP      TCGA-NJ-A4YQ      TCGA-NJ-A55A 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-NJ-A55O      TCGA-NJ-A55R      TCGA-O1-A52J 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
D30V12, continuous
                 vv
clus               R0  R1  R2  RX
  STK19 MUTATED     4   0   0   0
  STK19 WILD-TYPE 306  11   4  25
D30V13, multiclass
    clus
vv   STK19 MUTATED STK19 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK19 MUTATED                                  0     0
  STK19 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK19 MUTATED                           0     5
  STK19 WILD-TYPE                        29   372
D30V14, multiclass
                                  clus
vv                                 STK19 MUTATED STK19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, binary
                 cls
clus                0   1
  STK19 MUTATED     0   5
  STK19 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      0    5
  STK19 WILD-TYPE    6  344
                        clus
vv                       STK19 MUTATED STK19 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(31) Variable = NUDT11 MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     4   1
  NUDT11 WILD-TYPE 298 154
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              452 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               1              154 
$`NUDT11 MUTATED`
TCGA-44-7671 TCGA-44-A47F TCGA-50-5933 TCGA-67-4679 TCGA-86-8076 
       29.23        11.08        78.67        14.73        32.65 

$`NUDT11 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
        7.17        36.07        18.87        29.00        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
        3.25         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       40.60        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       50.33       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
        0.79        22.82        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        6.35        10.09        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
           11.08             0.00 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           78.67           238.29 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           29.23            19.79 
[1] "11.1 - 78.7 (29.2)" "0.0 - 238.3 (19.8)"
[1] "hr=" "2.3"
D31V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NUDT11 MUTATED         0        1        1         0         1          0
  NUDT11 WILD-TYPE       4      122      131        47        65         70
                  vv
clus               STAGE IIIB STAGE IV
  NUDT11 MUTATED            1        0
  NUDT11 WILD-TYPE         10       25
D31V3, multiclass
            clus
vv           NUDT11 MUTATED NUDT11 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                1              131
  STAGE IIA               0               47
  STAGE IIB               1               65
  STAGE IIIA              0               70
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUDT11 MUTATED     1   2   1   1
  NUDT11 WILD-TYPE 154 259  42  17
D31V4, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  T1              1              154
  T2              2              259
  T3              1               42
  T4              1               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
  NUDT11 MUTATED     3   1     1
  NUDT11 WILD-TYPE 304  88    71
D31V5, multiclass
       clus
vv      NUDT11 MUTATED NUDT11 WILD-TYPE
  N0                 3              304
  N1                 1               88
  N2+N3              1               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     5   0
  NUDT11 WILD-TYPE 323  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      5    0
  NUDT11 WILD-TYPE  323   23
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              5              323
  1              0               23
[1] 2 2
[1] FALSE
D31V7, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   5
  NUDT11 WILD-TYPE 259 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    5
  NUDT11 WILD-TYPE  259  216
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              0              259
  MALE                5              216
[1] 2 2
[1] FALSE
D31V8, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     3   1
  NUDT11 WILD-TYPE 330  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      3    1
  NUDT11 WILD-TYPE  330   48
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               3              330
  YES              1               48
[1] 2 2
[1] FALSE
D31V9, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2              115 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-44-3396 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-3918       TCGA-44-4112       TCGA-44-6144       TCGA-44-6147 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6775       TCGA-44-7660       TCGA-49-4486       TCGA-49-4494 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4505       TCGA-49-4506       TCGA-49-4510       TCGA-49-6742 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-6743       TCGA-49-6744       TCGA-53-7624       TCGA-53-A4EZ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7573       TCGA-55-7725       TCGA-55-7910 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8089       TCGA-55-8096       TCGA-55-8205 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8507       TCGA-55-8508       TCGA-55-8511 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8619       TCGA-55-8620       TCGA-55-8621 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491       TCGA-55-A492 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1677       TCGA-64-1681       TCGA-64-5775 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4670       TCGA-73-4676       TCGA-73-4677 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-6562       TCGA-86-6851       TCGA-86-7701       TCGA-86-7711 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7953       TCGA-86-7954 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7955       TCGA-86-8054       TCGA-86-8055       TCGA-86-8056 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8073       TCGA-86-8074       TCGA-86-8075       TCGA-86-8278 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8280       TCGA-86-8281       TCGA-86-8358 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6829 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-6849       TCGA-93-7347       TCGA-93-7348       TCGA-93-8067 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-95-7567       TCGA-99-7458 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NUDT11 MUTATED                            0                                 1
  NUDT11 WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NUDT11 MUTATED                                                    3
  NUDT11 WILD-TYPE                                                292
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NUDT11 MUTATED                                            0
  NUDT11 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NUDT11 MUTATED                                               0
  NUDT11 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  NUDT11 MUTATED                                0
  NUDT11 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  NUDT11 MUTATED                                    0
  NUDT11 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NUDT11 MUTATED                              0                             1
  NUDT11 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NUDT11 MUTATED                                               0
  NUDT11 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  NUDT11 MUTATED                              0
  NUDT11 WILD-TYPE                            9
D31V10, multiclass
                                                    clus
vv                                                   NUDT11 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   NUDT11 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               1              332 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-05-4382 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4384       TCGA-05-4389       TCGA-05-4390       TCGA-05-4396 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4397       TCGA-05-4398       TCGA-05-4405       TCGA-05-4410 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4415       TCGA-05-4417       TCGA-05-4418       TCGA-05-4420 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4422       TCGA-05-4424       TCGA-05-4425       TCGA-05-4426 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4427       TCGA-05-4430       TCGA-05-4432       TCGA-05-4433 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4434       TCGA-05-5420       TCGA-05-5423       TCGA-05-5425 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-5428       TCGA-35-4122       TCGA-35-4123       TCGA-35-5375 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-38-4625       TCGA-38-4626       TCGA-38-4629       TCGA-38-4631 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-38-4632       TCGA-38-7271       TCGA-38-A44F       TCGA-44-2656 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-2657       TCGA-44-3396       TCGA-44-3398       TCGA-44-3918 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-4112       TCGA-44-5643       TCGA-44-5644       TCGA-44-5645 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6144       TCGA-44-6145       TCGA-44-6146       TCGA-44-6148 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6774       TCGA-44-6775       TCGA-44-6776       TCGA-44-6777 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6778       TCGA-44-6779       TCGA-44-7659       TCGA-44-7660 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-7661       TCGA-44-7662       TCGA-44-7667       TCGA-44-7669 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-7670       TCGA-44-7672       TCGA-44-8117       TCGA-44-8119 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-8120       TCGA-44-A479       TCGA-44-A47A       TCGA-44-A47B 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-A47G       TCGA-44-A4SS       TCGA-44-A4SU       TCGA-49-4486 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4487       TCGA-49-4490       TCGA-49-4494       TCGA-49-4505 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4506       TCGA-49-4507       TCGA-49-4510       TCGA-49-4514 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-6742       TCGA-49-6743       TCGA-49-6744       TCGA-49-6745 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-6761       TCGA-49-6767       TCGA-50-5051       TCGA-50-5072 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-50-5931       TCGA-50-5939       TCGA-50-5941       TCGA-50-5942 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-50-6590       TCGA-50-7109       TCGA-50-8457       TCGA-50-8459 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-53-7624       TCGA-53-7626       TCGA-53-7813       TCGA-53-A4EZ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-6543       TCGA-55-6971       TCGA-55-6983       TCGA-55-6985 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7281       TCGA-55-7283       TCGA-55-7574       TCGA-55-7724 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7726       TCGA-55-7728       TCGA-55-7903 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7907       TCGA-55-7910       TCGA-55-7911       TCGA-55-7914 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7994       TCGA-55-7995       TCGA-55-8089       TCGA-55-8092 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8094       TCGA-55-8096       TCGA-55-8097       TCGA-55-8203 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8205       TCGA-55-8208       TCGA-55-8299       TCGA-55-8301 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8302       TCGA-55-8507       TCGA-55-8511       TCGA-55-8512 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8514       TCGA-55-8614       TCGA-55-8615       TCGA-55-8620 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8621       TCGA-55-A48X       TCGA-55-A48Y       TCGA-55-A48Z 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A491       TCGA-55-A492       TCGA-55-A493 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A494       TCGA-55-A4DF       TCGA-55-A4DG       TCGA-62-8398 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-8399       TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-A46S       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-1676       TCGA-64-1677       TCGA-64-1679       TCGA-64-5774 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-5775       TCGA-64-5778       TCGA-64-5779       TCGA-64-5781 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-5815       TCGA-69-7761       TCGA-69-7763       TCGA-69-7764 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-69-7973       TCGA-69-7974       TCGA-69-7978       TCGA-69-7979 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-69-7980       TCGA-69-8253       TCGA-69-8254       TCGA-69-8255 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-69-A59K       TCGA-73-4658       TCGA-73-4659       TCGA-73-4662 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4666       TCGA-73-4668       TCGA-73-4670       TCGA-73-4675 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4676       TCGA-73-7498       TCGA-75-5122       TCGA-75-5125 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-75-5126       TCGA-75-6203       TCGA-75-6206       TCGA-75-6207 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-75-6211       TCGA-75-6214       TCGA-75-7027       TCGA-75-7031 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7145       TCGA-78-7146       TCGA-78-7147       TCGA-78-7148 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7149       TCGA-78-7150       TCGA-78-7152       TCGA-78-7153 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7154       TCGA-78-7155       TCGA-78-7156       TCGA-78-7158 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7159       TCGA-78-7160       TCGA-78-7161       TCGA-78-7162 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7163       TCGA-78-7166       TCGA-78-7167       TCGA-78-7220 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7535       TCGA-78-7536       TCGA-78-7537       TCGA-78-7539 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7542       TCGA-78-7633       TCGA-78-8640       TCGA-78-8648 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-8655       TCGA-78-8660       TCGA-78-8662       TCGA-80-5607 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-80-5608       TCGA-80-5611       TCGA-83-5908       TCGA-86-6851 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7714       TCGA-86-7954 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8054       TCGA-86-8055       TCGA-86-8056       TCGA-86-8073 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8669       TCGA-86-8673       TCGA-86-8674       TCGA-91-6829 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-6830       TCGA-91-6835       TCGA-91-6836       TCGA-91-6840 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-6849       TCGA-91-7771       TCGA-91-8499       TCGA-91-A4BC 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-7347       TCGA-93-7348       TCGA-93-8067       TCGA-93-A4JN 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-A4JO       TCGA-95-7039       TCGA-95-7043       TCGA-95-7562 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-7944       TCGA-95-7947       TCGA-95-7948       TCGA-95-A4VK 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-A4VN       TCGA-95-A4VP       TCGA-97-7546       TCGA-97-7547 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-7552       TCGA-97-7553       TCGA-97-7554       TCGA-97-7937 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-7938       TCGA-97-7941       TCGA-97-8171       TCGA-97-8172 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-8174       TCGA-97-8176       TCGA-97-8179       TCGA-97-A4LX 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-A4M0       TCGA-97-A4M1       TCGA-97-A4M2       TCGA-97-A4M3 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-A4M5       TCGA-97-A4M7       TCGA-99-7458       TCGA-99-8025 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-99-8028       TCGA-99-8032       TCGA-J2-8194       TCGA-J2-A4AD 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6       TCGA-L9-A443 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-L9-A444       TCGA-MP-A4SV       TCGA-MP-A4SW       TCGA-MP-A4SY 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4T2       TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T7 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4T8       TCGA-MP-A4T9       TCGA-MP-A4TA       TCGA-MP-A4TC 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TD       TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TI       TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YF 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-NJ-A4YG       TCGA-NJ-A4YI       TCGA-NJ-A4YP       TCGA-NJ-A4YQ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-NJ-A55A       TCGA-NJ-A55O       TCGA-NJ-A55R       TCGA-O1-A52J 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
D31V12, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               1              256 
      TCGA-05-4384       TCGA-05-4390       TCGA-05-4396       TCGA-05-4405 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4410       TCGA-05-4415       TCGA-05-4417       TCGA-05-4424 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4427       TCGA-05-4433       TCGA-05-5420       TCGA-05-5423 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-5425       TCGA-05-5428       TCGA-35-4122       TCGA-35-4123 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-35-5375       TCGA-38-4625       TCGA-38-4626       TCGA-38-7271 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-38-A44F       TCGA-44-2656       TCGA-44-2657       TCGA-44-3396 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-3398       TCGA-44-3918       TCGA-44-4112       TCGA-44-5644 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-5645       TCGA-44-6144       TCGA-44-6145       TCGA-44-6147 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6148       TCGA-44-6774       TCGA-44-6775       TCGA-44-6776 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6777       TCGA-44-6778       TCGA-44-6779       TCGA-44-7659 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-7660       TCGA-44-7661       TCGA-44-7662       TCGA-44-7667 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-7669       TCGA-44-7670       TCGA-44-7672       TCGA-44-8117 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-8119       TCGA-44-8120       TCGA-44-A479       TCGA-44-A47A 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-A47B       TCGA-44-A47G       TCGA-44-A4SS       TCGA-44-A4SU 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4494       TCGA-49-4505       TCGA-53-7624 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-53-7626       TCGA-53-7813       TCGA-53-A4EZ       TCGA-55-1592 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-1595       TCGA-55-5899       TCGA-55-6642       TCGA-55-6712 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-6971       TCGA-55-7227       TCGA-55-7283       TCGA-55-7570 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7574       TCGA-55-7576       TCGA-55-7724       TCGA-55-7725 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7726       TCGA-55-7728       TCGA-55-7907       TCGA-55-7910 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7911       TCGA-55-7914       TCGA-55-8089       TCGA-55-8092 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8094       TCGA-55-8096       TCGA-55-8097       TCGA-55-8205 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8299       TCGA-55-8301       TCGA-55-8302       TCGA-55-8506 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8511       TCGA-55-8512       TCGA-55-8514 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8615       TCGA-55-8620       TCGA-55-8621       TCGA-55-A48X 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A492       TCGA-55-A493       TCGA-55-A494       TCGA-62-8398 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1681       TCGA-64-5774       TCGA-64-5775 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-5778       TCGA-64-5779       TCGA-64-5781       TCGA-69-7761 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-69-7763       TCGA-69-7764       TCGA-69-7765       TCGA-69-7974 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-69-7979       TCGA-69-8253       TCGA-69-8255       TCGA-69-A59K 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4670       TCGA-73-4675       TCGA-73-4676       TCGA-73-7498 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-75-6214       TCGA-75-7025       TCGA-75-7027       TCGA-75-7031 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7145       TCGA-78-7146       TCGA-78-7147       TCGA-78-7148 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7149       TCGA-78-7150       TCGA-78-7152       TCGA-78-7153 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7154       TCGA-78-7155       TCGA-78-7156       TCGA-78-7158 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7159       TCGA-78-7160       TCGA-78-7161       TCGA-78-7162 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7163       TCGA-78-7166       TCGA-78-7167       TCGA-78-7220 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7535       TCGA-78-7536       TCGA-78-7537       TCGA-78-7539 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7542       TCGA-78-7633       TCGA-78-8640       TCGA-78-8648 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-8655       TCGA-78-8660       TCGA-78-8662       TCGA-80-5607 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-80-5608       TCGA-83-5908       TCGA-86-6851       TCGA-86-7711 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-8054       TCGA-86-8055 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8073       TCGA-86-8074       TCGA-86-8281 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8669       TCGA-86-8673 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8674       TCGA-86-A456       TCGA-91-6829       TCGA-91-6830 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-6836       TCGA-91-6840       TCGA-91-6849       TCGA-91-8499 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-A4BC       TCGA-93-7347       TCGA-93-7348       TCGA-93-8067 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-93-A4JQ       TCGA-95-7043 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-7562       TCGA-95-7567       TCGA-95-7944       TCGA-95-7947 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-7948       TCGA-95-A4VK       TCGA-95-A4VN       TCGA-95-A4VP 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-7546       TCGA-97-7553       TCGA-97-7554       TCGA-97-7941 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-8171       TCGA-97-8172       TCGA-97-8174       TCGA-97-8176 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-8179       TCGA-97-A4LX       TCGA-97-A4M0       TCGA-97-A4M1 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-A4M2       TCGA-97-A4M3       TCGA-97-A4M5       TCGA-97-A4M7 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-99-7458       TCGA-99-8025       TCGA-99-8028       TCGA-99-8032 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-J2-8194       TCGA-J2-A4AD       TCGA-J2-A4AG       TCGA-L4-A4E5 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-L4-A4E6       TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5       TCGA-MP-A4SV       TCGA-MP-A4SW 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4T2       TCGA-MP-A4T4       TCGA-MP-A4T7       TCGA-MP-A4T8 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4T9       TCGA-MP-A4TA       TCGA-MP-A4TC       TCGA-MP-A4TE 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI       TCGA-MP-A4TK 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A5C7       TCGA-NJ-A4YG       TCGA-NJ-A4YI       TCGA-O1-A52J 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
                  vv
clus                R0  R1  R2  RX
  NUDT11 MUTATED     2   0   0   0
  NUDT11 WILD-TYPE 308  11   4  25
D31V13, multiclass
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2              348 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-05-4382 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4384       TCGA-05-4389       TCGA-05-4390       TCGA-05-4395 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4396       TCGA-05-4397       TCGA-05-4398       TCGA-05-4402 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4403       TCGA-05-4405       TCGA-05-4410       TCGA-05-4415 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4417       TCGA-05-4418       TCGA-05-4420       TCGA-05-4422 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4424       TCGA-05-4425       TCGA-05-4426       TCGA-05-4427 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4430       TCGA-05-4432       TCGA-05-4433       TCGA-05-4434 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-5420       TCGA-05-5423       TCGA-05-5425       TCGA-05-5428 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-5429       TCGA-05-5715       TCGA-35-4122       TCGA-35-4123 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-35-5375       TCGA-38-4625       TCGA-38-4626       TCGA-38-4627 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-38-4628       TCGA-38-4629       TCGA-38-4630       TCGA-38-4631 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-38-4632       TCGA-38-6178       TCGA-38-7271       TCGA-38-A44F 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-2657       TCGA-44-2661       TCGA-44-2665       TCGA-44-3396 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-3398       TCGA-44-3918       TCGA-44-3919       TCGA-44-4112 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6144       TCGA-44-6148       TCGA-44-6775       TCGA-44-A479 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-A47A       TCGA-44-A47B       TCGA-44-A47G       TCGA-44-A4SU 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4487       TCGA-49-4488       TCGA-49-4494 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4501       TCGA-49-4505       TCGA-49-4506       TCGA-49-4507 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4510       TCGA-49-4512       TCGA-49-4514       TCGA-49-6742 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-6744       TCGA-49-6761       TCGA-49-6767       TCGA-50-5051 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-50-5055       TCGA-50-5066       TCGA-50-5931       TCGA-50-5942 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-50-5944       TCGA-50-6593       TCGA-50-6597       TCGA-50-6673 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-50-8460       TCGA-53-7624       TCGA-53-7626       TCGA-53-A4EZ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-1592       TCGA-55-5899       TCGA-55-6642       TCGA-55-6970 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-6971       TCGA-55-6972       TCGA-55-6980       TCGA-55-6981 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-6983       TCGA-55-6985       TCGA-55-7281       TCGA-55-7284 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7570       TCGA-55-7574       TCGA-55-7576       TCGA-55-7724 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7726       TCGA-55-7727       TCGA-55-7728 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7815       TCGA-55-7903       TCGA-55-7907       TCGA-55-7910 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7911       TCGA-55-7914       TCGA-55-7994       TCGA-55-7995 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8085       TCGA-55-8087       TCGA-55-8089       TCGA-55-8090 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8091       TCGA-55-8092       TCGA-55-8094       TCGA-55-8097 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8203       TCGA-55-8204       TCGA-55-8205       TCGA-55-8206 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8207       TCGA-55-8208       TCGA-55-8299       TCGA-55-8301 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8302       TCGA-55-8505       TCGA-55-8506       TCGA-55-8507 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8508       TCGA-55-8510       TCGA-55-8511       TCGA-55-8512 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8513       TCGA-55-8514       TCGA-55-8614       TCGA-55-8615 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8616       TCGA-55-8619       TCGA-55-8620       TCGA-55-8621 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A48X       TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A491       TCGA-55-A492       TCGA-55-A493       TCGA-55-A494 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A4DF       TCGA-55-A4DG       TCGA-62-8394       TCGA-62-8395 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1676       TCGA-64-1677 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-1679       TCGA-64-1681       TCGA-64-5774       TCGA-64-5775 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-5778       TCGA-64-5779       TCGA-64-5781       TCGA-64-5815 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-67-3771       TCGA-67-3773       TCGA-67-6215       TCGA-67-6216 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-67-6217       TCGA-71-6725       TCGA-71-8520       TCGA-73-4658 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4670       TCGA-73-4675       TCGA-73-4676       TCGA-73-4677 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-75-5125 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-75-5126       TCGA-75-5146       TCGA-75-5147       TCGA-75-6203 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-75-6205       TCGA-75-6206       TCGA-75-6207       TCGA-75-6211 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-75-6212       TCGA-75-6214       TCGA-75-7025       TCGA-75-7027 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-75-7030       TCGA-75-7031       TCGA-78-7143       TCGA-78-7145 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7146       TCGA-78-7147       TCGA-78-7148       TCGA-78-7149 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7150       TCGA-78-7152       TCGA-78-7153       TCGA-78-7154 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7155       TCGA-78-7156       TCGA-78-7158       TCGA-78-7159 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7160       TCGA-78-7161       TCGA-78-7162       TCGA-78-7163 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7166       TCGA-78-7167       TCGA-78-7220       TCGA-78-7535 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7536       TCGA-78-7537       TCGA-78-7539       TCGA-78-7540 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7542       TCGA-78-7633       TCGA-78-8640       TCGA-78-8648 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-8655       TCGA-78-8660       TCGA-78-8662       TCGA-80-5607 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-80-5608       TCGA-80-5611       TCGA-83-5908       TCGA-86-6562 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7953       TCGA-86-7954       TCGA-86-7955       TCGA-86-8054 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8073       TCGA-86-8074 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8075       TCGA-86-8278       TCGA-86-8279       TCGA-86-8280 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8585       TCGA-86-8668 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8669       TCGA-86-8671       TCGA-86-8672       TCGA-86-8673 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8674       TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-6828       TCGA-91-6829       TCGA-91-6835       TCGA-91-6840 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-A4BD       TCGA-93-7347       TCGA-93-7348       TCGA-93-8067 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-93-A4JP       TCGA-93-A4JQ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-7562       TCGA-95-7944       TCGA-95-7947       TCGA-95-7948 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-8039       TCGA-95-A4VK       TCGA-95-A4VN       TCGA-97-7546 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-7554       TCGA-97-7938       TCGA-97-7941       TCGA-97-8176 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-A4M2       TCGA-97-A4M7       TCGA-99-7458       TCGA-99-8025 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-99-8028       TCGA-99-8032       TCGA-99-8033       TCGA-J2-A4AD 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-J2-A4AE       TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1       TCGA-MN-A4N4 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MN-A4N5       TCGA-MP-A4SV       TCGA-MP-A4SW       TCGA-MP-A4SY 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4T2       TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T7 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4T8       TCGA-MP-A4T9       TCGA-MP-A4TA       TCGA-MP-A4TC 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TD       TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TI       TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YQ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUDT11 MUTATED                                  0     0
  NUDT11 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUDT11 MUTATED                           1     4
  NUDT11 WILD-TYPE                        28   373
D31V14, multiclass
                                  clus
vv                                 NUDT11 MUTATED NUDT11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         4              373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V15, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   5
  NUDT11 WILD-TYPE   6 344
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    5
  NUDT11 WILD-TYPE    6  344
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              5              344
[1] 2 2
[1] FALSE

Clustering(32) Variable = SLAMF9 MUTATION ANALYSIS
D32V1, survival
                  sevent
clus2                0   1
  SLAMF9 MUTATED     7   5
  SLAMF9 WILD-TYPE 295 150
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
              12              445 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
               5              150 
$`SLAMF9 MUTATED`
TCGA-44-3918 TCGA-50-5930 TCGA-53-7624 TCGA-55-1592 TCGA-55-8506 TCGA-55-8507 
       34.06         9.27        34.29        23.05         0.36         0.26 
TCGA-78-7539 TCGA-86-8075 TCGA-86-8358 TCGA-95-7567 TCGA-97-7554 TCGA-L9-A443 
       26.01        22.82        21.47        18.67        25.48         6.35 

$`SLAMF9 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       38.10        42.77        37.15        38.24        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       15.72        60.16        31.04        49.28         8.09        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.99         7.59        27.25        30.54        13.94        35.21 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.95         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        17.16         2.01         6.90 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        82.68        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
       88.14        26.53        31.20         8.02        53.33        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57        24.33         0.79        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.20        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
       17.29        41.82        16.54         2.86        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       31.69        64.60        63.52        43.79         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
            0.26             0.00 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
           34.29           238.29 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
          22.145           19.760 
[1] "0.3 - 34.3 (22.1)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.9"
D32V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLAMF9 MUTATED         0        4        2         1         2          2
  SLAMF9 WILD-TYPE       4      119      130        46        64         68
                  vv
clus               STAGE IIIB STAGE IV
  SLAMF9 MUTATED            0        1
  SLAMF9 WILD-TYPE         11       24
D32V3, multiclass
            clus
vv           SLAMF9 MUTATED SLAMF9 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              119
  STAGE IB                2              130
  STAGE IIA               1               46
  STAGE IIB               2               64
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLAMF9 MUTATED     3   8   1   0
  SLAMF9 WILD-TYPE 152 253  42  18
D32V4, multiclass
    clus
vv   SLAMF9 MUTATED SLAMF9 WILD-TYPE
  T1              3              152
  T2              8              253
  T3              1               42
  T4              0               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
  SLAMF9 MUTATED     9   1     2
  SLAMF9 WILD-TYPE 298  88    70
D32V5, multiclass
       clus
vv      SLAMF9 MUTATED SLAMF9 WILD-TYPE
  N0                 9              298
  N1                 1               88
  N2+N3              2               70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     8   1
  SLAMF9 WILD-TYPE 320  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      8    1
  SLAMF9 WILD-TYPE  320   22
   clus
vv  SLAMF9 MUTATED SLAMF9 WILD-TYPE
  0              8              320
  1              1               22
[1] 2 2
[1] FALSE
D32V7, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     7   5
  SLAMF9 WILD-TYPE 252 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      7    5
  SLAMF9 WILD-TYPE  252  216
        clus
vv       SLAMF9 MUTATED SLAMF9 WILD-TYPE
  FEMALE              7              252
  MALE                5              216
[1] 2 2
[1] FALSE
D32V8, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     9   1
  SLAMF9 WILD-TYPE 324  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      9    1
  SLAMF9 WILD-TYPE  324   48
     clus
vv    SLAMF9 MUTATED SLAMF9 WILD-TYPE
  NO               9              324
  YES              1               48
[1] 2 2
[1] FALSE
D32V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLAMF9 MUTATED                            0                                 3
  SLAMF9 WILD-TYPE                         18                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLAMF9 MUTATED                                                    8
  SLAMF9 WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SLAMF9 MUTATED                                            0
  SLAMF9 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SLAMF9 MUTATED                                               0
  SLAMF9 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  SLAMF9 MUTATED                                0
  SLAMF9 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  SLAMF9 MUTATED                                    0
  SLAMF9 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SLAMF9 MUTATED                              0                             1
  SLAMF9 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SLAMF9 MUTATED                                               0
  SLAMF9 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  SLAMF9 MUTATED                              0
  SLAMF9 WILD-TYPE                            9
D32V10, multiclass
                                                    clus
vv                                                   SLAMF9 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   SLAMF9 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
D32V12, continuous
                  vv
clus                R0  R1  R2  RX
  SLAMF9 MUTATED    10   0   0   0
  SLAMF9 WILD-TYPE 300  11   4  25
D32V13, multiclass
    clus
vv   SLAMF9 MUTATED SLAMF9 WILD-TYPE
  R0             10              300
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLAMF9 MUTATED                                  0     0
  SLAMF9 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLAMF9 MUTATED                           0    12
  SLAMF9 WILD-TYPE                        29   365
D32V14, multiclass
                                  clus
vv                                 SLAMF9 MUTATED SLAMF9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        12              365
[1] 4 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
  SLAMF9 MUTATED     1  10
  SLAMF9 WILD-TYPE   5 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      1   10
  SLAMF9 WILD-TYPE    5  339
                        clus
vv                       SLAMF9 MUTATED SLAMF9 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             10              339
[1] 2 2
[1] FALSE

Clustering(33) Variable = DNMT3A MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2                0   1
  DNMT3A MUTATED    13   5
  DNMT3A WILD-TYPE 289 150
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              18              439 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               5              150 
$`DNMT3A MUTATED`
TCGA-44-7662 TCGA-50-5931 TCGA-50-6595 TCGA-55-6987 TCGA-55-8089 TCGA-55-8207 
        7.17        14.27         6.21        70.26         3.29         2.17 
TCGA-55-A490 TCGA-64-5774 TCGA-64-5778 TCGA-86-8073 TCGA-86-8672 TCGA-91-6830 
        1.58        87.98        42.90        24.33         0.62         1.97 
TCGA-91-8499 TCGA-97-7547 TCGA-97-8176 TCGA-97-8179 TCGA-MP-A4TA TCGA-NJ-A4YQ 
        1.18        64.60        15.39        14.30        31.23        29.13 

$`DNMT3A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       24.99        40.54       107.21         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
       21.40        18.18        19.89        31.69        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
        5.39        18.12        16.41        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        41.59         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  DNMT3A MUTATED DNMT3A WILD-TYPE 
            0.62             0.00 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           87.98           238.29 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
          14.285           19.820 
[1] "0.6 - 88.0 (14.3)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.2"
D33V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DNMT3A MUTATED         0        6        7         2         1          2
  DNMT3A WILD-TYPE       4      117      125        45        65         68
                  vv
clus               STAGE IIIB STAGE IV
  DNMT3A MUTATED            0        0
  DNMT3A WILD-TYPE         11       25
D33V3, multiclass
            clus
vv           DNMT3A MUTATED DNMT3A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                6              117
  STAGE IB                7              125
  STAGE IIA               2               45
  STAGE IIB               1               65
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNMT3A MUTATED     7   9   2   0
  DNMT3A WILD-TYPE 148 252  41  18
D33V4, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  T1              7              148
  T2              9              252
  T3              2               41
  T4              0               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
  DNMT3A MUTATED    15   2     1
  DNMT3A WILD-TYPE 292  87    71
D33V5, multiclass
       clus
vv      DNMT3A MUTATED DNMT3A WILD-TYPE
  N0                15              292
  N1                 2               87
  N2+N3              1               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                  cls
clus                 0   1
  DNMT3A MUTATED    12   0
  DNMT3A WILD-TYPE 316  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED     12    0
  DNMT3A WILD-TYPE  316   23
   clus
vv  DNMT3A MUTATED DNMT3A WILD-TYPE
  0             12              316
  1              0               23
[1] 2 2
[1] FALSE
D33V7, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     7  11
  DNMT3A WILD-TYPE 252 210
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      7   11
  DNMT3A WILD-TYPE  252  210
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE              7              252
  MALE               11              210
[1] 2 2
[1] FALSE
D33V8, binary
                  cls
clus                 0   1
  DNMT3A MUTATED    13   2
  DNMT3A WILD-TYPE 320  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED     13    2
  DNMT3A WILD-TYPE  320   47
     clus
vv    DNMT3A MUTATED DNMT3A WILD-TYPE
  NO              13              320
  YES              2               47
[1] 2 2
[1] FALSE
D33V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DNMT3A MUTATED                            3                                 0
  DNMT3A WILD-TYPE                         15                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DNMT3A MUTATED                                                   12
  DNMT3A WILD-TYPE                                                283
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DNMT3A MUTATED                                            0
  DNMT3A WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DNMT3A MUTATED                                               2
  DNMT3A WILD-TYPE                                            17
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  DNMT3A MUTATED                                0
  DNMT3A WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  DNMT3A MUTATED                                    0
  DNMT3A WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DNMT3A MUTATED                              0                             1
  DNMT3A WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DNMT3A MUTATED                                               0
  DNMT3A WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  DNMT3A MUTATED                              0
  DNMT3A WILD-TYPE                            9
D33V10, multiclass
                                                    clus
vv                                                   DNMT3A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   2
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   DNMT3A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    17
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
D33V12, continuous
                  vv
clus                R0  R1  R2  RX
  DNMT3A MUTATED    10   0   0   1
  DNMT3A WILD-TYPE 300  11   4  24
D33V13, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  R0             10              300
  R1              0               11
  R2              0                4
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNMT3A MUTATED                                  0     0
  DNMT3A WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNMT3A MUTATED                           0    18
  DNMT3A WILD-TYPE                        29   359
D33V14, multiclass
                                  clus
vv                                 DNMT3A MUTATED DNMT3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        18              359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     0  18
  DNMT3A WILD-TYPE   6 331
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      0   18
  DNMT3A WILD-TYPE    6  331
                        clus
vv                       DNMT3A MUTATED DNMT3A WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             18              331
[1] 2 2
[1] FALSE

Clustering(34) Variable = CTNNB1 MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    14   4
  CTNNB1 WILD-TYPE 288 151
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              18              439 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               4              151 
$`CTNNB1 MUTATED`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4422 TCGA-05-4425 TCGA-44-4112 TCGA-44-A47A 
       14.01        45.01        12.00        21.99        26.56        15.32 
TCGA-55-8085 TCGA-55-A48Y TCGA-62-A46V TCGA-62-A470 TCGA-67-3771 TCGA-67-4679 
       29.72        20.71        72.30        39.25        20.05        14.73 
TCGA-69-7979 TCGA-78-7153 TCGA-78-7158 TCGA-86-8280 TCGA-97-8171 TCGA-MP-A4SV 
        2.93       119.51         5.88        23.05        18.67        86.14 

$`CTNNB1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        19.96        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 
       14.96         9.01        29.98        30.02        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        44.42        38.10        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       34.06        33.73        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       13.74        12.66         3.25         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.33        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94        35.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 
        6.48        17.65         6.15        19.82         0.16        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       22.65        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       54.35        67.96        13.61        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.41        51.25        28.47        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         4.41        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        38.50        32.09        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
        6.35        10.09        27.19        38.63         2.76        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            2.93             0.00 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          119.51           238.29 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           21.35            19.73 
[1] "2.9 - 119.5 (21.4)" "0.0 - 238.3 (19.7)"
[1] "hr=" "2.1"
D34V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CTNNB1 MUTATED         0        3        8         2         0          2
  CTNNB1 WILD-TYPE       4      120      124        45        66         68
                  vv
clus               STAGE IIIB STAGE IV
  CTNNB1 MUTATED            1        2
  CTNNB1 WILD-TYPE         10       23
D34V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                8              124
  STAGE IIA               2               45
  STAGE IIB               0               66
  STAGE IIIA              2               68
  STAGE IIIB              1               10
  STAGE IV                2               23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNNB1 MUTATED     3  14   1   1
  CTNNB1 WILD-TYPE 152 247  42  17
D34V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              3              152
  T2             14              247
  T3              1               42
  T4              1               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
  CTNNB1 MUTATED    15   0     4
  CTNNB1 WILD-TYPE 292  89    68
D34V5, multiclass
       clus
vv      CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0                15              292
  N1                 0               89
  N2+N3              4               68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    15   2
  CTNNB1 WILD-TYPE 313  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     15    2
  CTNNB1 WILD-TYPE  313   21
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             15              313
  1              2               21
[1] 2 2
[1] FALSE
D34V7, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    10   9
  CTNNB1 WILD-TYPE 249 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     10    9
  CTNNB1 WILD-TYPE  249  212
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE             10              249
  MALE                9              212
[1] 2 2
[1] FALSE
D34V8, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    13   1
  CTNNB1 WILD-TYPE 320  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     13    1
  CTNNB1 WILD-TYPE  320   48
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              13              320
  YES              1               48
[1] 2 2
[1] FALSE
D34V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CTNNB1 MUTATED                            2                                 7
  CTNNB1 WILD-TYPE                         16                                94
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CTNNB1 MUTATED                                                    7
  CTNNB1 WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CTNNB1 MUTATED                                            0
  CTNNB1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CTNNB1 MUTATED                                               1
  CTNNB1 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  CTNNB1 MUTATED                                0
  CTNNB1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  CTNNB1 MUTATED                                    0
  CTNNB1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CTNNB1 MUTATED                              0                             2
  CTNNB1 WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CTNNB1 MUTATED                                               0
  CTNNB1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  CTNNB1 MUTATED                              0
  CTNNB1 WILD-TYPE                            9
D34V10, multiclass
                                                    clus
vv                                                   CTNNB1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   CTNNB1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
D34V12, continuous
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED    14   2   0   1
  CTNNB1 WILD-TYPE 296   9   4  24
D34V13, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             14              296
  R1              2                9
  R2              0                4
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNB1 MUTATED                                  0     1
  CTNNB1 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED                           1    11
  CTNNB1 WILD-TYPE                        28   366
D34V14, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        11              366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     0  11
  CTNNB1 WILD-TYPE   6 338
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0   11
  CTNNB1 WILD-TYPE    6  338
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             11              338
[1] 2 2
[1] FALSE

Clustering(35) Variable = PTPRU MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2               0   1
  PTPRU MUTATED    13   5
  PTPRU WILD-TYPE 289 150
  PTPRU MUTATED PTPRU WILD-TYPE 
             18             439 
  PTPRU MUTATED PTPRU WILD-TYPE 
              5             150 
$`PTPRU MUTATED`
TCGA-05-4397 TCGA-05-4420 TCGA-44-8117 TCGA-49-6744 TCGA-55-6982 TCGA-55-7995 
       24.03        29.98        12.66        55.33        32.71         0.16 
TCGA-55-8506 TCGA-62-A46O TCGA-67-3771 TCGA-69-7978 TCGA-73-4668 TCGA-78-7539 
        0.36        47.80        20.05         4.41        15.35        26.01 
TCGA-86-8279 TCGA-91-6829 TCGA-91-6836 TCGA-91-8499 TCGA-J2-A4AD TCGA-MN-A4N4 
       31.20        41.36        13.71         1.18        18.08        38.63 

$`PTPRU WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96         9.01        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 
       18.87        29.00        29.23        13.74         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       55.89        16.04        53.29        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        7.79         2.20        45.34        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 
        0.53         6.48        17.65         6.15        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        49.25        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        2.04        42.90        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
       29.46        24.23        13.64        26.47        10.62         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60        14.27         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       24.30        23.80        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        6.35        10.09        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  PTPRU MUTATED PTPRU WILD-TYPE 
           0.16            0.00 
  PTPRU MUTATED PTPRU WILD-TYPE 
          55.33          238.29 
  PTPRU MUTATED PTPRU WILD-TYPE 
          22.04           19.76 
[1] "0.2 - 55.3 (22.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.1"
D35V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PTPRU MUTATED         0        5        5         3         5          0
  PTPRU WILD-TYPE       4      118      127        44        61         70
                 vv
clus              STAGE IIIB STAGE IV
  PTPRU MUTATED            0        0
  PTPRU WILD-TYPE         11       25
D35V3, multiclass
            clus
vv           PTPRU MUTATED PTPRU WILD-TYPE
  STAGE I                0               4
  STAGE IA               5             118
  STAGE IB               5             127
  STAGE IIA              3              44
  STAGE IIB              5              61
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRU MUTATED     5  12   1   0
  PTPRU WILD-TYPE 150 249  42  18
D35V4, multiclass
    clus
vv   PTPRU MUTATED PTPRU WILD-TYPE
  T1             5             150
  T2            12             249
  T3             1              42
  T4             0              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
  PTPRU MUTATED    12   6     0
  PTPRU WILD-TYPE 295  83    72
D35V5, multiclass
       clus
vv      PTPRU MUTATED PTPRU WILD-TYPE
  N0               12             295
  N1                6              83
  N2+N3             0              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                 cls
clus                0   1
  PTPRU MUTATED    11   0
  PTPRU WILD-TYPE 317  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED     11    0
  PTPRU WILD-TYPE  317   23
   clus
vv  PTPRU MUTATED PTPRU WILD-TYPE
  0            11             317
  1             0              23
[1] 2 2
[1] FALSE
D35V7, binary
                 cls
clus                0   1
  PTPRU MUTATED    12   6
  PTPRU WILD-TYPE 247 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED     12    6
  PTPRU WILD-TYPE  247  215
        clus
vv       PTPRU MUTATED PTPRU WILD-TYPE
  FEMALE            12             247
  MALE               6             215
[1] 2 2
[1] FALSE
D35V8, binary
                 cls
clus                0   1
  PTPRU MUTATED    12   1
  PTPRU WILD-TYPE 321  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED     12    1
  PTPRU WILD-TYPE  321   48
     clus
vv    PTPRU MUTATED PTPRU WILD-TYPE
  NO             12             321
  YES             1              48
[1] 2 2
[1] FALSE
D35V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PTPRU MUTATED                            0                                 5
  PTPRU WILD-TYPE                         18                                96
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PTPRU MUTATED                                                   11
  PTPRU WILD-TYPE                                                284
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PTPRU MUTATED                                            0
  PTPRU WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PTPRU MUTATED                                               1
  PTPRU WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PTPRU MUTATED                                0
  PTPRU WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PTPRU MUTATED                                    1
  PTPRU WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PTPRU MUTATED                              0                             0
  PTPRU WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PTPRU MUTATED                                               0
  PTPRU WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PTPRU MUTATED                              0
  PTPRU WILD-TYPE                            9
D35V10, multiclass
                                                    clus
vv                                                   PTPRU MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PTPRU WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
D35V12, continuous
                 vv
clus               R0  R1  R2  RX
  PTPRU MUTATED    12   0   0   1
  PTPRU WILD-TYPE 298  11   4  24
D35V13, multiclass
    clus
vv   PTPRU MUTATED PTPRU WILD-TYPE
  R0            12             298
  R1             0              11
  R2             0               4
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRU MUTATED                                  1     0
  PTPRU WILD-TYPE                                0     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRU MUTATED                           1    14
  PTPRU WILD-TYPE                        28   363
D35V14, multiclass
                                  clus
vv                                 PTPRU MUTATED PTPRU WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       14             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, binary
                 cls
clus                0   1
  PTPRU MUTATED     0  13
  PTPRU WILD-TYPE   6 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED      0   13
  PTPRU WILD-TYPE    6  336
                        clus
vv                       PTPRU MUTATED PTPRU WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            13             336
[1] 2 2
[1] FALSE

Clustering(36) Variable = PIK3CA MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    14  12
  PIK3CA WILD-TYPE 288 143
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              431 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              143 
$`PIK3CA MUTATED`
TCGA-05-4249 TCGA-05-4397 TCGA-44-5643 TCGA-44-5645 TCGA-44-7670 TCGA-49-6743 
       50.07        24.03        33.30        28.01        29.00        53.29 
TCGA-50-5044 TCGA-50-6590 TCGA-50-6592 TCGA-55-7574 TCGA-55-7724 TCGA-55-7995 
       20.52        42.35        25.55         3.12        23.18         0.16 
TCGA-55-8092 TCGA-64-1677 TCGA-73-7499 TCGA-78-7146 TCGA-78-7153 TCGA-86-7714 
        5.06        20.65        50.33         5.69       119.51        20.55 
TCGA-93-7348 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-97-8177 TCGA-97-8552 
       17.46         2.86        15.68        15.65        16.41        20.58 
TCGA-MP-A4SY TCGA-MP-A4TI 
       49.35        14.10 

$`PIK3CA WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       37.15        38.24        34.06        33.73        26.56        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       19.46        12.03         7.17        36.07        18.87        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        16.04 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5045 TCGA-50-5049 
       55.33        17.16        11.64        22.26        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 
        9.37        29.03        25.12        22.55         3.91        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 
        1.15         7.99         0.20         0.13         1.32         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 
        0.53         6.48        17.65         6.15        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.66        19.73         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        56.81        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24        17.16         2.01         6.90        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
        1.25        39.09       163.10        27.16        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
      129.53        21.90        39.95        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        38.04        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       26.50        29.46        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN 
        1.18         1.45        19.82        22.45         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
        1.08        19.00        17.29        41.82        16.54        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       12.39        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       15.39        14.30        21.60        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.16             0.00 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          119.51           238.29 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          20.615           19.660 
[1] "0.2 - 119.5 (20.6)" "0.0 - 238.3 (19.7)"
[1] "hr=" "1.2"
D36V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PIK3CA MUTATED         1        4        9         3         4          6
  PIK3CA WILD-TYPE       3      119      123        44        62         64
                  vv
clus               STAGE IIIB STAGE IV
  PIK3CA MUTATED            1        0
  PIK3CA WILD-TYPE         10       25
D36V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 1                3
  STAGE IA                4              119
  STAGE IB                9              123
  STAGE IIA               3               44
  STAGE IIB               4               62
  STAGE IIIA              6               64
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3CA MUTATED     8  18   1   1
  PIK3CA WILD-TYPE 147 243  42  17
D36V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              8              147
  T2             18              243
  T3              1               42
  T4              1               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
  PIK3CA MUTATED    14   7     6
  PIK3CA WILD-TYPE 293  82    66
D36V5, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  N0                14              293
  N1                 7               82
  N2+N3              6               66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    22   0
  PIK3CA WILD-TYPE 306  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     22    0
  PIK3CA WILD-TYPE  306   23
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             22              306
  1              0               23
[1] 2 2
[1] FALSE
D36V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    20   8
  PIK3CA WILD-TYPE 239 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     20    8
  PIK3CA WILD-TYPE  239  213
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             20              239
  MALE                8              213
[1] 2 2
[1] FALSE
D36V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    21   3
  PIK3CA WILD-TYPE 312  46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     21    3
  PIK3CA WILD-TYPE  312   46
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              21              312
  YES              3               46
[1] 2 2
[1] FALSE
D36V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PIK3CA MUTATED                            0                                 8
  PIK3CA WILD-TYPE                         18                                93
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                   18
  PIK3CA WILD-TYPE                                                277
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PIK3CA MUTATED                                            0
  PIK3CA WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PIK3CA MUTATED                                               1
  PIK3CA WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  PIK3CA MUTATED                                1
  PIK3CA WILD-TYPE                              1
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  PIK3CA MUTATED                                    0
  PIK3CA WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PIK3CA MUTATED                              0                             0
  PIK3CA WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PIK3CA MUTATED                                               0
  PIK3CA WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  PIK3CA MUTATED                              0
  PIK3CA WILD-TYPE                            9
D36V10, multiclass
                                                    clus
vv                                                   PIK3CA MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             18
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   PIK3CA WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                93
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
D36V12, continuous
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    17   1   0   1
  PIK3CA WILD-TYPE 293  10   4  24
D36V13, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             17              293
  R1              1               10
  R2              0                4
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     0
  PIK3CA WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           4    20
  PIK3CA WILD-TYPE                        25   357
D36V14, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     4               25
  WHITE                                        20              357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  20
  PIK3CA WILD-TYPE   5 329
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   20
  PIK3CA WILD-TYPE    5  329
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             20              329
[1] 2 2
[1] FALSE

Clustering(37) Variable = ZNF608 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2                0   1
  ZNF608 MUTATED     5   4
  ZNF608 WILD-TYPE 297 151
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               9              448 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               4              151 
$`ZNF608 MUTATED`
TCGA-05-4415 TCGA-44-7667 TCGA-55-8203 TCGA-55-8299 TCGA-86-8054 TCGA-91-6831 
        2.99        36.07        17.98        15.42        37.74        10.19 
TCGA-91-8497 TCGA-95-7562 TCGA-97-A4M5 
       14.27         2.86        20.84 

$`ZNF608 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51         2.17        22.16         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       50.33       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        35.24         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36         1.97         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8499 
       27.68         7.36         1.15        16.18        16.60         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
        1.08        19.00        17.29        41.82        16.54        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  ZNF608 MUTATED ZNF608 WILD-TYPE 
            2.86             0.00 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
           37.74           238.29 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
           15.42            19.82 
[1] "2.9 - 37.7 (15.4)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "2.1"
D37V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZNF608 MUTATED         0        4        1         1         2          0
  ZNF608 WILD-TYPE       4      119      131        46        64         70
                  vv
clus               STAGE IIIB STAGE IV
  ZNF608 MUTATED            1        0
  ZNF608 WILD-TYPE         10       25
D37V3, multiclass
            clus
vv           ZNF608 MUTATED ZNF608 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              119
  STAGE IB                1              131
  STAGE IIA               1               46
  STAGE IIB               2               64
  STAGE IIIA              0               70
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF608 MUTATED     4   3   1   1
  ZNF608 WILD-TYPE 151 258  42  17
D37V4, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  T1              4              151
  T2              3              258
  T3              1               42
  T4              1               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
  ZNF608 MUTATED     6   2     1
  ZNF608 WILD-TYPE 301  87    71
D37V5, multiclass
       clus
vv      ZNF608 MUTATED ZNF608 WILD-TYPE
  N0                 6              301
  N1                 2               87
  N2+N3              1               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     5   0
  ZNF608 WILD-TYPE 323  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      5    0
  ZNF608 WILD-TYPE  323   23
   clus
vv  ZNF608 MUTATED ZNF608 WILD-TYPE
  0              5              323
  1              0               23
[1] 2 2
[1] FALSE
D37V7, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     4   5
  ZNF608 WILD-TYPE 255 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      4    5
  ZNF608 WILD-TYPE  255  216
        clus
vv       ZNF608 MUTATED ZNF608 WILD-TYPE
  FEMALE              4              255
  MALE                5              216
[1] 2 2
[1] FALSE
D37V8, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     9   0
  ZNF608 WILD-TYPE 324  49
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      9    0
  ZNF608 WILD-TYPE  324   49
     clus
vv    ZNF608 MUTATED ZNF608 WILD-TYPE
  NO               9              324
  YES              0               49
[1] 2 2
[1] FALSE
D37V9, continuous
[1] "Remove cluster labels:" "ZNF608 MUTATED"        
clus
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               1              116 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-44-3396 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-44-3918       TCGA-44-4112       TCGA-44-6144       TCGA-44-6147 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-44-6775       TCGA-44-7660       TCGA-44-A47F       TCGA-49-4486 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-49-4494       TCGA-49-4505       TCGA-49-4506       TCGA-49-4510 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-49-6742       TCGA-49-6743       TCGA-49-6744       TCGA-53-7624 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-53-A4EZ       TCGA-55-7283       TCGA-55-7573       TCGA-55-7725 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-7910       TCGA-55-7914       TCGA-55-8089       TCGA-55-8096 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-8205       TCGA-55-8208       TCGA-55-8507       TCGA-55-8508 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-8511       TCGA-55-8512       TCGA-55-8619       TCGA-55-8620 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-8621       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-A492       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-64-5775       TCGA-64-5778       TCGA-69-7974       TCGA-69-8254 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-71-6725       TCGA-71-8520       TCGA-73-4659       TCGA-73-4662 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-73-4666       TCGA-73-4668       TCGA-73-4670       TCGA-73-4676 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-73-4677       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-6562       TCGA-86-6851       TCGA-86-7701 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-7711       TCGA-86-7713       TCGA-86-7714       TCGA-86-7953 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8055       TCGA-86-8056 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-8073       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8280       TCGA-86-8281 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8668       TCGA-86-8669 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-8671       TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-91-6829       TCGA-91-6849       TCGA-93-7347       TCGA-93-7348 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-95-7567 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-99-7458       TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF608 MUTATED                            1                                 2
  ZNF608 WILD-TYPE                         17                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF608 MUTATED                                                    6
  ZNF608 WILD-TYPE                                                289
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZNF608 MUTATED                                            0
  ZNF608 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZNF608 MUTATED                                               0
  ZNF608 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ZNF608 MUTATED                                0
  ZNF608 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ZNF608 MUTATED                                    0
  ZNF608 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZNF608 MUTATED                              0                             0
  ZNF608 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZNF608 MUTATED                                               0
  ZNF608 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ZNF608 MUTATED                              0
  ZNF608 WILD-TYPE                            9
D37V10, multiclass
                                                    clus
vv                                                   ZNF608 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ZNF608 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
D37V12, continuous
                  vv
clus                R0  R1  R2  RX
  ZNF608 MUTATED     4   0   0   1
  ZNF608 WILD-TYPE 306  11   4  24
D37V13, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  R0              4              306
  R1              0               11
  R2              0                4
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF608 MUTATED                                  0     0
  ZNF608 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF608 MUTATED                           1     7
  ZNF608 WILD-TYPE                        28   370
D37V14, multiclass
                                  clus
vv                                 ZNF608 MUTATED ZNF608 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         7              370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     0   8
  ZNF608 WILD-TYPE   6 341
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      0    8
  ZNF608 WILD-TYPE    6  341
                        clus
vv                       ZNF608 MUTATED ZNF608 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              8              341
[1] 2 2
[1] FALSE

Clustering(38) Variable = STIM1 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2               0   1
  STIM1 MUTATED     8   1
  STIM1 WILD-TYPE 294 154
  STIM1 MUTATED STIM1 WILD-TYPE 
              9             448 
  STIM1 MUTATED STIM1 WILD-TYPE 
              1             154 
$`STIM1 MUTATED`
TCGA-05-4427 TCGA-35-4123 TCGA-44-2656 TCGA-55-8510 TCGA-69-7979 TCGA-78-8640 
       26.01         5.98        46.98        17.72         2.93       232.18 
TCGA-86-8673 TCGA-95-7043 TCGA-NJ-A4YG 
       28.34        16.54        62.60 

$`STIM1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 
        0.76         0.95         0.36         0.26         0.49         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        6.90        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55        50.24        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
        1.15        13.91        30.84        27.58         0.62        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29        41.82         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        71.05         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  STIM1 MUTATED STIM1 WILD-TYPE 
           2.93            0.00 
  STIM1 MUTATED STIM1 WILD-TYPE 
         232.18          238.29 
  STIM1 MUTATED STIM1 WILD-TYPE 
          26.01           19.79 
[1] "2.9 - 232.2 (26.0)" "0.0 - 238.3 (19.8)"
[1] "hr=" "5.2"
D38V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  STIM1 MUTATED         0        2        5         1         1          0
  STIM1 WILD-TYPE       4      121      127        46        65         70
                 vv
clus              STAGE IIIB STAGE IV
  STIM1 MUTATED            0        0
  STIM1 WILD-TYPE         11       25
D38V3, multiclass
            clus
vv           STIM1 MUTATED STIM1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               5             127
  STAGE IIA              1              46
  STAGE IIB              1              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STIM1 MUTATED     3   6   0   0
  STIM1 WILD-TYPE 152 255  43  18
D38V4, multiclass
    clus
vv   STIM1 MUTATED STIM1 WILD-TYPE
  T1             3             152
  T2             6             255
  T3             0              43
  T4             0              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
  STIM1 MUTATED     7   2     0
  STIM1 WILD-TYPE 300  87    72
D38V5, multiclass
       clus
vv      STIM1 MUTATED STIM1 WILD-TYPE
  N0                7             300
  N1                2              87
  N2+N3             0              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                 cls
clus                0   1
  STIM1 MUTATED     6   0
  STIM1 WILD-TYPE 322  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      6    0
  STIM1 WILD-TYPE  322   23
   clus
vv  STIM1 MUTATED STIM1 WILD-TYPE
  0             6             322
  1             0              23
[1] 2 2
[1] FALSE
D38V7, binary
                 cls
clus                0   1
  STIM1 MUTATED     4   5
  STIM1 WILD-TYPE 255 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      4    5
  STIM1 WILD-TYPE  255  216
        clus
vv       STIM1 MUTATED STIM1 WILD-TYPE
  FEMALE             4             255
  MALE               5             216
[1] 2 2
[1] FALSE
D38V8, binary
                 cls
clus                0   1
  STIM1 MUTATED     7   0
  STIM1 WILD-TYPE 326  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      7    0
  STIM1 WILD-TYPE  326   49
     clus
vv    STIM1 MUTATED STIM1 WILD-TYPE
  NO              7             326
  YES             0              49
[1] 2 2
[1] FALSE
D38V9, continuous
[1] "Remove cluster labels:" "STIM1 MUTATED"         
clus
  STIM1 MUTATED STIM1 WILD-TYPE 
              1             116 
     TCGA-35-4122      TCGA-35-5375      TCGA-44-3396      TCGA-44-3918 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-44-4112      TCGA-44-6144      TCGA-44-6147      TCGA-44-6775 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-44-7660      TCGA-44-A47F      TCGA-49-4486      TCGA-49-4494 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4510      TCGA-49-6742 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-49-6743      TCGA-49-6744      TCGA-53-7624      TCGA-53-A4EZ 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-8621 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5775 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4676      TCGA-73-4677 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-6562      TCGA-86-6851      TCGA-86-7701      TCGA-86-7711 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7953      TCGA-86-7954 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-7955      TCGA-86-8054      TCGA-86-8055      TCGA-86-8056 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8073      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8280      TCGA-86-8281 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-91-6829      TCGA-91-6849      TCGA-93-7347      TCGA-93-7348 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-99-7458      TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STIM1 MUTATED                            1                                 2
  STIM1 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STIM1 MUTATED                                                    5
  STIM1 WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STIM1 MUTATED                                            0
  STIM1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STIM1 MUTATED                                               1
  STIM1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  STIM1 MUTATED                                0
  STIM1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  STIM1 MUTATED                                    0
  STIM1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STIM1 MUTATED                              0                             0
  STIM1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STIM1 MUTATED                                               0
  STIM1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  STIM1 MUTATED                              0
  STIM1 WILD-TYPE                            9
D38V10, multiclass
                                                    clus
vv                                                   STIM1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   STIM1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
D38V12, continuous
                 vv
clus               R0  R1  R2  RX
  STIM1 MUTATED     5   0   0   0
  STIM1 WILD-TYPE 305  11   4  25
D38V13, multiclass
    clus
vv   STIM1 MUTATED STIM1 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STIM1 MUTATED                                  0     0
  STIM1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STIM1 MUTATED                           0     7
  STIM1 WILD-TYPE                        29   370
D38V14, multiclass
                                  clus
vv                                 STIM1 MUTATED STIM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V15, binary
                 cls
clus                0   1
  STIM1 MUTATED     0   6
  STIM1 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      0    6
  STIM1 WILD-TYPE    6  343
                        clus
vv                       STIM1 MUTATED STIM1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(39) Variable = EMG1 MUTATION ANALYSIS
D39V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     3   1
  EMG1 WILD-TYPE 299 154
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            453 
  EMG1 MUTATED EMG1 WILD-TYPE 
             1            154 
$`EMG1 MUTATED`
TCGA-44-2656 TCGA-44-3919 TCGA-67-3773 TCGA-69-8254 
       46.98        33.73        14.04        13.45 

$`EMG1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        38.24        34.06        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K 
        4.41         2.93        12.56        14.01         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       50.33       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  EMG1 MUTATED EMG1 WILD-TYPE 
         13.45           0.00 
  EMG1 MUTATED EMG1 WILD-TYPE 
         46.98         238.29 
  EMG1 MUTATED EMG1 WILD-TYPE 
        23.885         19.820 
[1] "13.4 - 47.0 (23.9)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.5"
D39V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  EMG1 MUTATED         0        1        2         0         1          0
  EMG1 WILD-TYPE       4      122      130        47        65         70
                vv
clus             STAGE IIIB STAGE IV
  EMG1 MUTATED            0        0
  EMG1 WILD-TYPE         11       25
D39V3, multiclass
            clus
vv           EMG1 MUTATED EMG1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              2            130
  STAGE IIA             0             47
  STAGE IIB             1             65
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EMG1 MUTATED     1   4   0   0
  EMG1 WILD-TYPE 154 257  43  18
D39V4, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  T1            1            154
  T2            4            257
  T3            0             43
  T4            0             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
  EMG1 MUTATED     3   1     0
  EMG1 WILD-TYPE 304  88    72
D39V5, multiclass
       clus
vv      EMG1 MUTATED EMG1 WILD-TYPE
  N0               3            304
  N1               1             88
  N2+N3            0             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                cls
clus               0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 324  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  324   23
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            4            324
  1            0             23
[1] 2 2
[1] FALSE
D39V7, binary
                cls
clus               0   1
  EMG1 MUTATED     3   2
  EMG1 WILD-TYPE 256 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      3    2
  EMG1 WILD-TYPE  256  219
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            3            256
  MALE              2            219
[1] 2 2
[1] FALSE
D39V8, binary
                cls
clus               0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 329  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  329   49
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             4            329
  YES            0             49
[1] 2 2
[1] FALSE
D39V9, continuous
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             1            116 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-44-3396 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-6144     TCGA-44-6147 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-44-A47F     TCGA-49-4486 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-49-4494     TCGA-49-4505     TCGA-49-4506     TCGA-49-4510 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-49-6742     TCGA-49-6743     TCGA-49-6744     TCGA-53-7624 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-53-A4EZ     TCGA-55-7283     TCGA-55-7573     TCGA-55-7725 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7914     TCGA-55-8089     TCGA-55-8096 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8208     TCGA-55-8507     TCGA-55-8508 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8619     TCGA-55-8620 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8621     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-69-7974     TCGA-71-6725 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4676     TCGA-73-4677 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-6562     TCGA-86-6851     TCGA-86-7701     TCGA-86-7711 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7953     TCGA-86-7954 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-7955     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8280     TCGA-86-8281 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6849     TCGA-93-7347     TCGA-93-7348 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-95-7567 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-99-7458     TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  EMG1 MUTATED                            0                                 1
  EMG1 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  EMG1 MUTATED                                                    4
  EMG1 WILD-TYPE                                                291
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  EMG1 MUTATED                                            0
  EMG1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  EMG1 MUTATED                                               0
  EMG1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  EMG1 MUTATED                                0
  EMG1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  EMG1 MUTATED                                    0
  EMG1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  EMG1 MUTATED                              0                             0
  EMG1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  EMG1 MUTATED                                               0
  EMG1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  EMG1 MUTATED                              0
  EMG1 WILD-TYPE                            9
D39V10, multiclass
                                                    clus
vv                                                   EMG1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   EMG1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
D39V12, continuous
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             2            255 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4417     TCGA-05-4424 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4433     TCGA-05-5420     TCGA-05-5423 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-35-4122     TCGA-35-4123 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-7271 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2657     TCGA-44-3396     TCGA-44-3398 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-5644     TCGA-44-5645 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-6144     TCGA-44-6145     TCGA-44-6147     TCGA-44-6148 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-6774     TCGA-44-6775     TCGA-44-6776     TCGA-44-6777 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-6778     TCGA-44-6779     TCGA-44-7659     TCGA-44-7660 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-7661     TCGA-44-7662     TCGA-44-7667     TCGA-44-7669 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-7670     TCGA-44-7672     TCGA-44-8117     TCGA-44-8119 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS     TCGA-44-A4SU 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4494     TCGA-49-4505     TCGA-53-7624 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ     TCGA-55-1592 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-1595     TCGA-55-5899     TCGA-55-6642     TCGA-55-6712 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-6971     TCGA-55-7227     TCGA-55-7283     TCGA-55-7570 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7724     TCGA-55-7725 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7728     TCGA-55-7907     TCGA-55-7910 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7911     TCGA-55-7914     TCGA-55-8089     TCGA-55-8092 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8096     TCGA-55-8097     TCGA-55-8205 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8506 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8511     TCGA-55-8512     TCGA-55-8514 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8615     TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A493     TCGA-55-A494     TCGA-62-8398 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1681     TCGA-64-5774     TCGA-64-5775 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5779     TCGA-64-5781     TCGA-69-7761 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-69-7763     TCGA-69-7764     TCGA-69-7765     TCGA-69-7974 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-69-7979     TCGA-69-8253     TCGA-69-8255     TCGA-69-A59K 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4675     TCGA-73-4676     TCGA-73-7498 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-75-6214     TCGA-75-7025     TCGA-75-7027     TCGA-75-7031 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7145     TCGA-78-7146     TCGA-78-7147     TCGA-78-7148 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7149     TCGA-78-7150     TCGA-78-7152     TCGA-78-7153 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7154     TCGA-78-7155     TCGA-78-7156     TCGA-78-7158 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7159     TCGA-78-7160     TCGA-78-7161     TCGA-78-7162 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7163     TCGA-78-7166     TCGA-78-7167     TCGA-78-7220 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7535     TCGA-78-7536     TCGA-78-7537     TCGA-78-7539 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7542     TCGA-78-7633     TCGA-78-8640     TCGA-78-8648 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8660     TCGA-78-8662     TCGA-80-5608 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6851     TCGA-86-7711     TCGA-86-7714 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8281     TCGA-86-8358 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8669     TCGA-86-8673     TCGA-86-8674 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-A456     TCGA-91-6829     TCGA-91-6830     TCGA-91-6836 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-91-6840     TCGA-91-6849     TCGA-91-8499     TCGA-91-A4BC 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043     TCGA-95-7562 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-95-7567     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7941     TCGA-97-8171 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4T2 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  EMG1 MUTATED     3   0   0   0
  EMG1 WILD-TYPE 307  11   4  25
D39V13, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  R0            3            307
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EMG1 MUTATED                                  0     0
  EMG1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED                           0     4
  EMG1 WILD-TYPE                        29   373
D39V14, multiclass
                                  clus
vv                                 EMG1 MUTATED EMG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       4            373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, binary
                cls
clus               0   1
  EMG1 MUTATED     0   4
  EMG1 WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    4
  EMG1 WILD-TYPE    6  345
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            345
[1] 2 2
[1] FALSE

Clustering(40) Variable = PHKA1 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2               0   1
  PHKA1 MUTATED     9   3
  PHKA1 WILD-TYPE 293 152
  PHKA1 MUTATED PHKA1 WILD-TYPE 
             12             445 
  PHKA1 MUTATED PHKA1 WILD-TYPE 
              3             152 
$`PHKA1 MUTATED`
TCGA-44-8117 TCGA-49-6767 TCGA-53-7626 TCGA-55-6970 TCGA-55-8506 TCGA-62-8399 
       12.66        22.26        30.54        15.25         0.36        88.64 
TCGA-64-1679 TCGA-67-3771 TCGA-78-7161 TCGA-86-7954 TCGA-86-8358 TCGA-L4-A4E5 
       81.80        20.05         9.57        19.89        21.47        19.00 

$`PHKA1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        11.64        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
       36.99         7.59        27.25        34.29        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       42.51        40.73         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        42.38        14.60        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1681 
       39.25        40.96        29.92        56.81        20.65        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24        17.16         2.01         6.90        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        50.33       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       32.78        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
       23.80        18.08        35.47        32.48        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  PHKA1 MUTATED PHKA1 WILD-TYPE 
           0.36            0.00 
  PHKA1 MUTATED PHKA1 WILD-TYPE 
          88.64          238.29 
  PHKA1 MUTATED PHKA1 WILD-TYPE 
          19.97           19.76 
[1] "0.4 - 88.6 (20.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.6"
D40V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PHKA1 MUTATED         1        1        3         1         3          3
  PHKA1 WILD-TYPE       3      122      129        46        63         67
                 vv
clus              STAGE IIIB STAGE IV
  PHKA1 MUTATED            0        0
  PHKA1 WILD-TYPE         11       25
D40V3, multiclass
            clus
vv           PHKA1 MUTATED PHKA1 WILD-TYPE
  STAGE I                1               3
  STAGE IA               1             122
  STAGE IB               3             129
  STAGE IIA              1              46
  STAGE IIB              3              63
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PHKA1 MUTATED     4   5   3   0
  PHKA1 WILD-TYPE 151 256  40  18
D40V4, multiclass
    clus
vv   PHKA1 MUTATED PHKA1 WILD-TYPE
  T1             4             151
  T2             5             256
  T3             3              40
  T4             0              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
  PHKA1 MUTATED     8   1     3
  PHKA1 WILD-TYPE 299  88    69
D40V5, multiclass
       clus
vv      PHKA1 MUTATED PHKA1 WILD-TYPE
  N0                8             299
  N1                1              88
  N2+N3             3              69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                 cls
clus                0   1
  PHKA1 MUTATED     9   0
  PHKA1 WILD-TYPE 319  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED      9    0
  PHKA1 WILD-TYPE  319   23
   clus
vv  PHKA1 MUTATED PHKA1 WILD-TYPE
  0             9             319
  1             0              23
[1] 2 2
[1] FALSE
D40V7, binary
                 cls
clus                0   1
  PHKA1 MUTATED    10   2
  PHKA1 WILD-TYPE 249 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED     10    2
  PHKA1 WILD-TYPE  249  219
        clus
vv       PHKA1 MUTATED PHKA1 WILD-TYPE
  FEMALE            10             249
  MALE               2             219
[1] 2 2
[1] FALSE
D40V8, binary
                 cls
clus                0   1
  PHKA1 MUTATED     8   0
  PHKA1 WILD-TYPE 325  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED      8    0
  PHKA1 WILD-TYPE  325   49
     clus
vv    PHKA1 MUTATED PHKA1 WILD-TYPE
  NO              8             325
  YES             0              49
[1] 2 2
[1] FALSE
D40V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PHKA1 MUTATED                            0                                 1
  PHKA1 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PHKA1 MUTATED                                                    8
  PHKA1 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PHKA1 MUTATED                                            0
  PHKA1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PHKA1 MUTATED                                               1
  PHKA1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PHKA1 MUTATED                                0
  PHKA1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PHKA1 MUTATED                                    0
  PHKA1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PHKA1 MUTATED                              0                             2
  PHKA1 WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PHKA1 MUTATED                                               0
  PHKA1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PHKA1 MUTATED                              0
  PHKA1 WILD-TYPE                            9
D40V10, multiclass
                                                    clus
vv                                                   PHKA1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PHKA1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
D40V12, continuous
                 vv
clus               R0  R1  R2  RX
  PHKA1 MUTATED     9   2   0   0
  PHKA1 WILD-TYPE 301   9   4  25
D40V13, multiclass
    clus
vv   PHKA1 MUTATED PHKA1 WILD-TYPE
  R0             9             301
  R1             2               9
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHKA1 MUTATED                                  0     0
  PHKA1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PHKA1 MUTATED                           1    11
  PHKA1 WILD-TYPE                        28   366
D40V14, multiclass
                                  clus
vv                                 PHKA1 MUTATED PHKA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V15, binary
                 cls
clus                0   1
  PHKA1 MUTATED     0   9
  PHKA1 WILD-TYPE   6 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED      0    9
  PHKA1 WILD-TYPE    6  340
                        clus
vv                       PHKA1 MUTATED PHKA1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(41) Variable = PAK1 MUTATION ANALYSIS
D41V1, survival
                sevent
clus2              0   1
  PAK1 MUTATED     4   4
  PAK1 WILD-TYPE 298 151
  PAK1 MUTATED PAK1 WILD-TYPE 
             8            449 
  PAK1 MUTATED PAK1 WILD-TYPE 
             4            151 
$`PAK1 MUTATED`
TCGA-49-6744 TCGA-78-7150 TCGA-78-7156 TCGA-86-7713 TCGA-86-8672 TCGA-91-6830 
       55.33        21.90        32.09        38.04         0.62         1.97 
TCGA-95-7562 TCGA-97-7553 
        2.86        43.79 

$`PAK1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94        35.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        20.58       129.53        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        38.50         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        31.13        34.39        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  PAK1 MUTATED PAK1 WILD-TYPE 
          0.62           0.00 
  PAK1 MUTATED PAK1 WILD-TYPE 
         55.33         238.29 
  PAK1 MUTATED PAK1 WILD-TYPE 
        26.995         19.760 
[1] "0.6 - 55.3 (27.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.4"
D41V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PAK1 MUTATED         0        2        0         4         2          0
  PAK1 WILD-TYPE       4      121      132        43        64         70
                vv
clus             STAGE IIIB STAGE IV
  PAK1 MUTATED            0        1
  PAK1 WILD-TYPE         11       24
D41V3, multiclass
            clus
vv           PAK1 MUTATED PAK1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              0            132
  STAGE IIA             4             43
  STAGE IIB             2             64
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAK1 MUTATED     3   4   1   1
  PAK1 WILD-TYPE 152 257  42  17
D41V4, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  T1            3            152
  T2            4            257
  T3            1             42
  T4            1             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
  PAK1 MUTATED     3   5     0
  PAK1 WILD-TYPE 304  84    72
D41V5, multiclass
       clus
vv      PAK1 MUTATED PAK1 WILD-TYPE
  N0               3            304
  N1               5             84
  N2+N3            0             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                cls
clus               0   1
  PAK1 MUTATED     5   1
  PAK1 WILD-TYPE 323  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      5    1
  PAK1 WILD-TYPE  323   22
   clus
vv  PAK1 MUTATED PAK1 WILD-TYPE
  0            5            323
  1            1             22
[1] 2 2
[1] FALSE
D41V7, binary
                cls
clus               0   1
  PAK1 MUTATED     3   6
  PAK1 WILD-TYPE 256 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      3    6
  PAK1 WILD-TYPE  256  215
        clus
vv       PAK1 MUTATED PAK1 WILD-TYPE
  FEMALE            3            256
  MALE              6            215
[1] 2 2
[1] FALSE
D41V8, binary
                cls
clus               0   1
  PAK1 MUTATED     7   0
  PAK1 WILD-TYPE 326  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      7    0
  PAK1 WILD-TYPE  326   49
     clus
vv    PAK1 MUTATED PAK1 WILD-TYPE
  NO             7            326
  YES            0             49
[1] 2 2
[1] FALSE
D41V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PAK1 MUTATED                            0                                 2
  PAK1 WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PAK1 MUTATED                                                    6
  PAK1 WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PAK1 MUTATED                                            0
  PAK1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PAK1 MUTATED                                               1
  PAK1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  PAK1 MUTATED                                0
  PAK1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  PAK1 MUTATED                                    0
  PAK1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PAK1 MUTATED                              0                             0
  PAK1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PAK1 MUTATED                                               0
  PAK1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  PAK1 MUTATED                              0
  PAK1 WILD-TYPE                            9
D41V10, multiclass
                                                    clus
vv                                                   PAK1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   PAK1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
D41V12, continuous
                vv
clus              R0  R1  R2  RX
  PAK1 MUTATED     5   0   0   1
  PAK1 WILD-TYPE 305  11   4  24
D41V13, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK1 MUTATED                                  0     0
  PAK1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK1 MUTATED                           1     8
  PAK1 WILD-TYPE                        28   369
D41V14, multiclass
                                  clus
vv                                 PAK1 MUTATED PAK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       8            369
[1] 4 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
  PAK1 MUTATED     0   6
  PAK1 WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      0    6
  PAK1 WILD-TYPE    6  343
                        clus
vv                       PAK1 MUTATED PAK1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(42) Variable = NRAS MUTATION ANALYSIS
D42V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     2   1
  NRAS WILD-TYPE 300 154
  NRAS MUTATED NRAS WILD-TYPE 
             3            454 
  NRAS MUTATED NRAS WILD-TYPE 
             1            154 
$`NRAS MUTATED`
TCGA-35-4123 TCGA-38-4632 TCGA-69-7979 
        5.98        44.61         2.93 

$`NRAS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         7.40         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       37.71        49.05        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  NRAS MUTATED NRAS WILD-TYPE 
          2.93           0.00 
  NRAS MUTATED NRAS WILD-TYPE 
         44.61         238.29 
  NRAS MUTATED NRAS WILD-TYPE 
          5.98          19.82 
[1] "2.9 - 44.6 (6.0)"   "0.0 - 238.3 (19.8)"
[1] "hr=" "1.3"
D42V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NRAS MUTATED         0        1        1         0         0          0
  NRAS WILD-TYPE       4      122      131        47        66         70
                vv
clus             STAGE IIIB STAGE IV
  NRAS MUTATED            0        1
  NRAS WILD-TYPE         11       24
D42V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              1            131
  STAGE IIA             0             47
  STAGE IIB             0             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NRAS MUTATED     1   2   0   0
  NRAS WILD-TYPE 154 259  43  18
D42V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            1            154
  T2            2            259
  T3            0             43
  T4            0             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
  NRAS MUTATED     2   1     0
  NRAS WILD-TYPE 305  88    72
D42V5, multiclass
       clus
vv      NRAS MUTATED NRAS WILD-TYPE
  N0               2            305
  N1               1             88
  N2+N3            0             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                cls
clus               0   1
  NRAS MUTATED     1   1
  NRAS WILD-TYPE 327  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    1
  NRAS WILD-TYPE  327   22
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0            1            327
  1            1             22
[1] 2 2
[1] FALSE
D42V7, binary
                cls
clus               0   1
  NRAS MUTATED     1   2
  NRAS WILD-TYPE 258 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    2
  NRAS WILD-TYPE  258  219
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            1            258
  MALE              2            219
[1] 2 2
[1] FALSE
D42V8, binary
                cls
clus               0   1
  NRAS MUTATED     1   0
  NRAS WILD-TYPE 332  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    0
  NRAS WILD-TYPE  332   49
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             1            332
  YES            0             49
[1] 2 2
[1] FALSE
D42V9, continuous
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1            116 
    TCGA-35-4122     TCGA-35-5375     TCGA-44-3396     TCGA-44-3918 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-4112     TCGA-44-6144     TCGA-44-6147     TCGA-44-6775 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-7660     TCGA-44-A47F     TCGA-49-4486     TCGA-49-4494 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4510     TCGA-49-6742 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-6743     TCGA-49-6744     TCGA-53-7624     TCGA-53-A4EZ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-8621 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5775 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4676     TCGA-73-4677 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-6562     TCGA-86-6851     TCGA-86-7701     TCGA-86-7711 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7953     TCGA-86-7954 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-7955     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8280     TCGA-86-8281 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6849     TCGA-93-7347     TCGA-93-7348 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-95-7567 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-99-7458     TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NRAS MUTATED                            1                                 0
  NRAS WILD-TYPE                         17                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NRAS MUTATED                                                    2
  NRAS WILD-TYPE                                                293
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NRAS MUTATED                                            0
  NRAS WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NRAS MUTATED                                               0
  NRAS WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  NRAS MUTATED                                0
  NRAS WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  NRAS MUTATED                                    0
  NRAS WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NRAS MUTATED                              0                             0
  NRAS WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NRAS MUTATED                                               0
  NRAS WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  NRAS MUTATED                              0
  NRAS WILD-TYPE                            9
D42V10, multiclass
                                                    clus
vv                                                   NRAS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   NRAS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
D42V12, continuous
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2            255 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4417     TCGA-05-4424 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4433     TCGA-05-5420     TCGA-05-5423 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-35-4122     TCGA-35-5375 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-7271     TCGA-38-A44F 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-2656     TCGA-44-2657     TCGA-44-3396     TCGA-44-3398 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-5644     TCGA-44-5645 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6144     TCGA-44-6145     TCGA-44-6147     TCGA-44-6148 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6774     TCGA-44-6775     TCGA-44-6776     TCGA-44-6777 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6778     TCGA-44-6779     TCGA-44-7659     TCGA-44-7660 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-7661     TCGA-44-7662     TCGA-44-7667     TCGA-44-7669 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-7670     TCGA-44-7672     TCGA-44-8117     TCGA-44-8119 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS     TCGA-44-A4SU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4486     TCGA-49-4494     TCGA-49-4505     TCGA-53-7624 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ     TCGA-55-1592 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-1595     TCGA-55-5899     TCGA-55-6642     TCGA-55-6712 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-6971     TCGA-55-7227     TCGA-55-7283     TCGA-55-7570 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7724     TCGA-55-7725 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7728     TCGA-55-7907     TCGA-55-7910 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7911     TCGA-55-7914     TCGA-55-8089     TCGA-55-8092 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8096     TCGA-55-8097     TCGA-55-8205 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8506 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8511     TCGA-55-8512     TCGA-55-8514 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8615     TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A493     TCGA-55-A494     TCGA-62-8398 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1681     TCGA-64-5774     TCGA-64-5775 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5779     TCGA-64-5781     TCGA-69-7761 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-69-7763     TCGA-69-7764     TCGA-69-7765     TCGA-69-7974 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-69-8253     TCGA-69-8255     TCGA-69-A59K     TCGA-73-4659 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-7498     TCGA-75-6214 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-7025     TCGA-75-7027     TCGA-75-7031     TCGA-78-7145 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7146     TCGA-78-7147     TCGA-78-7148     TCGA-78-7149 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7150     TCGA-78-7152     TCGA-78-7153     TCGA-78-7154 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7155     TCGA-78-7156     TCGA-78-7158     TCGA-78-7159 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7160     TCGA-78-7161     TCGA-78-7162     TCGA-78-7163 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7167     TCGA-78-7220     TCGA-78-7535 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7536     TCGA-78-7537     TCGA-78-7539     TCGA-78-7542 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6851     TCGA-86-7711     TCGA-86-7714 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-7954     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8281     TCGA-86-8358 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8669     TCGA-86-8673     TCGA-86-8674 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-A456     TCGA-91-6829     TCGA-91-6830     TCGA-91-6836 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-6840     TCGA-91-6849     TCGA-91-8499     TCGA-91-A4BC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043     TCGA-95-7562 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-95-7567     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7941     TCGA-97-8171 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4T2 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED     2   0   0   0
  NRAS WILD-TYPE 308  11   4  25
D42V13, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2            348 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4402 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4405     TCGA-05-4410     TCGA-05-4415 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4418     TCGA-05-4420     TCGA-05-4422 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4424     TCGA-05-4425     TCGA-05-4426     TCGA-05-4427 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-4434 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5425     TCGA-05-5428 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-5429     TCGA-05-5715     TCGA-35-4122     TCGA-35-5375 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-4627     TCGA-38-4628 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-38-4629     TCGA-38-4630     TCGA-38-4631     TCGA-38-6178 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-38-7271     TCGA-38-A44F     TCGA-44-2657     TCGA-44-2661 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-2665     TCGA-44-3396     TCGA-44-3398     TCGA-44-3918 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-3919     TCGA-44-4112     TCGA-44-6144     TCGA-44-6148 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6775     TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-A47G     TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4487 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4488     TCGA-49-4494     TCGA-49-4501     TCGA-49-4505 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4506     TCGA-49-4507     TCGA-49-4510     TCGA-49-4512 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4514     TCGA-49-6742     TCGA-49-6744     TCGA-49-6761 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-6767     TCGA-50-5051     TCGA-50-5055     TCGA-50-5066 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-50-5931     TCGA-50-5942     TCGA-50-5944     TCGA-50-6593 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-50-6597     TCGA-50-6673     TCGA-50-8460     TCGA-53-7624 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-53-7626     TCGA-53-A4EZ     TCGA-55-1592     TCGA-55-5899 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-6642     TCGA-55-6970     TCGA-55-6971     TCGA-55-6972 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-6980     TCGA-55-6981     TCGA-55-6983     TCGA-55-6985 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7281     TCGA-55-7284     TCGA-55-7570     TCGA-55-7574 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7576     TCGA-55-7724     TCGA-55-7725     TCGA-55-7726 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7727     TCGA-55-7728     TCGA-55-7815     TCGA-55-7903 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7907     TCGA-55-7910     TCGA-55-7911     TCGA-55-7914 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7994     TCGA-55-7995     TCGA-55-8085     TCGA-55-8087 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8090     TCGA-55-8091     TCGA-55-8092 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8097     TCGA-55-8203     TCGA-55-8204 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8206     TCGA-55-8207     TCGA-55-8208 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8505 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8508     TCGA-55-8510 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8513     TCGA-55-8514 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8614     TCGA-55-8615     TCGA-55-8616     TCGA-55-8619 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF     TCGA-55-A4DG 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-8394     TCGA-62-8395     TCGA-62-8397     TCGA-62-8398 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-1676     TCGA-64-1677     TCGA-64-1679     TCGA-64-1681 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-5774     TCGA-64-5775     TCGA-64-5778     TCGA-64-5779 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-5781     TCGA-64-5815     TCGA-67-3771     TCGA-67-3773 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-67-4679     TCGA-67-6215     TCGA-67-6216     TCGA-67-6217 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4658     TCGA-73-4659 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-4677     TCGA-73-7498 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-7499     TCGA-75-5122     TCGA-75-5125     TCGA-75-5126 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-5146     TCGA-75-5147     TCGA-75-6203     TCGA-75-6205 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-6206     TCGA-75-6207     TCGA-75-6211     TCGA-75-6212 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-6214     TCGA-75-7025     TCGA-75-7027     TCGA-75-7030 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-7031     TCGA-78-7143     TCGA-78-7145     TCGA-78-7146 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7147     TCGA-78-7148     TCGA-78-7149     TCGA-78-7150 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7152     TCGA-78-7153     TCGA-78-7154     TCGA-78-7155 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7156     TCGA-78-7158     TCGA-78-7159     TCGA-78-7160 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7161     TCGA-78-7162     TCGA-78-7163     TCGA-78-7166 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7167     TCGA-78-7220     TCGA-78-7535     TCGA-78-7536 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7537     TCGA-78-7539     TCGA-78-7540     TCGA-78-7542 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-80-5611     TCGA-83-5908     TCGA-86-6562     TCGA-86-7701 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-7711     TCGA-86-7713     TCGA-86-7714     TCGA-86-7953 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8054     TCGA-86-8055 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8075 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8280 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8585     TCGA-86-8668 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8671     TCGA-86-8672     TCGA-86-8673 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-6828     TCGA-91-6829     TCGA-91-6835     TCGA-91-6840 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-A4BD     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JP     TCGA-93-A4JQ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-95-8039     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-97-7546 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-7554     TCGA-97-7938     TCGA-97-7941     TCGA-97-8176 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M7     TCGA-99-7458     TCGA-99-8025 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-99-8028     TCGA-99-8032     TCGA-99-8033     TCGA-J2-A4AD 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-J2-A4AE     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4T8     TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TD     TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YQ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRAS MUTATED                                  0     0
  NRAS WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED                           1     2
  NRAS WILD-TYPE                        28   375
D42V14, multiclass
                                  clus
vv                                 NRAS MUTATED NRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       2            375
[1] 4 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
  NRAS MUTATED     0   3
  NRAS WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    3
  NRAS WILD-TYPE    6  346
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            346
[1] 2 2
[1] FALSE

Clustering(43) Variable = G3BP1 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  G3BP1 MUTATED     4   3
  G3BP1 WILD-TYPE 298 152
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              7             450 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              3             152 
$`G3BP1 MUTATED`
TCGA-05-4432 TCGA-44-2661 TCGA-49-4486 TCGA-50-5044 TCGA-50-6594 TCGA-53-A4EZ 
       25.02        38.10        76.21        20.52        12.16        35.21 
TCGA-67-3771 
       20.05 

$`G3BP1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       14.73        26.30         4.37        46.98        44.42        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 
       22.55        42.35         3.91        25.55        11.05         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       34.29        30.54        13.94        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       28.47        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  G3BP1 MUTATED G3BP1 WILD-TYPE 
          12.16            0.00 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
          76.21          238.29 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
         25.020          19.695 
[1] "12.2 - 76.2 (25.0)" "0.0 - 238.3 (19.7)"
[1] "hr=" "1"  
D43V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  G3BP1 MUTATED         0        3        0         1         1          2
  G3BP1 WILD-TYPE       4      120      132        46        65         68
                 vv
clus              STAGE IIIB STAGE IV
  G3BP1 MUTATED            1        0
  G3BP1 WILD-TYPE         10       25
D43V3, multiclass
            clus
vv           G3BP1 MUTATED G3BP1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               0             132
  STAGE IIA              1              46
  STAGE IIB              1              65
  STAGE IIIA             2              68
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  G3BP1 MUTATED     3   2   2   1
  G3BP1 WILD-TYPE 152 259  41  17
D43V4, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  T1             3             152
  T2             2             259
  T3             2              41
  T4             1              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
  G3BP1 MUTATED     3   3     2
  G3BP1 WILD-TYPE 304  86    70
D43V5, multiclass
       clus
vv      G3BP1 MUTATED G3BP1 WILD-TYPE
  N0                3             304
  N1                3              86
  N2+N3             2              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                 cls
clus                0   1
  G3BP1 MUTATED     7   0
  G3BP1 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      7    0
  G3BP1 WILD-TYPE  321   23
   clus
vv  G3BP1 MUTATED G3BP1 WILD-TYPE
  0             7             321
  1             0              23
[1] 2 2
[1] FALSE
D43V7, binary
                 cls
clus                0   1
  G3BP1 MUTATED     5   3
  G3BP1 WILD-TYPE 254 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      5    3
  G3BP1 WILD-TYPE  254  218
        clus
vv       G3BP1 MUTATED G3BP1 WILD-TYPE
  FEMALE             5             254
  MALE               3             218
[1] 2 2
[1] FALSE
D43V8, binary
                 cls
clus                0   1
  G3BP1 MUTATED     5   2
  G3BP1 WILD-TYPE 328  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      5    2
  G3BP1 WILD-TYPE  328   47
     clus
vv    G3BP1 MUTATED G3BP1 WILD-TYPE
  NO              5             328
  YES             2              47
[1] 2 2
[1] FALSE
D43V9, continuous
[1] "Remove cluster labels:" "G3BP1 MUTATED"         
clus
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              2             115 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-44-3396 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-6144      TCGA-44-6147 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-44-A47F      TCGA-49-4494 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4510      TCGA-49-6742 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-49-6743      TCGA-49-6744      TCGA-53-7624      TCGA-55-7283 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7573      TCGA-55-7725      TCGA-55-7910      TCGA-55-7914 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8205      TCGA-55-8208 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8511      TCGA-55-8512 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8620      TCGA-55-8621      TCGA-55-A48Z 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A491      TCGA-55-A492      TCGA-55-A494 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5775      TCGA-64-5778 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-8254      TCGA-71-6725      TCGA-71-8520 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-73-4670      TCGA-73-4676      TCGA-73-4677      TCGA-73-7498 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-73-7499      TCGA-75-5122      TCGA-83-5908      TCGA-86-6562 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-6851      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7953      TCGA-86-7954      TCGA-86-7955 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8054      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8280      TCGA-86-8281      TCGA-86-8358 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-91-6849      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567      TCGA-99-7458 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  G3BP1 MUTATED                            1                                 1
  G3BP1 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  G3BP1 MUTATED                                                    5
  G3BP1 WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  G3BP1 MUTATED                                            0
  G3BP1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  G3BP1 MUTATED                                               0
  G3BP1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  G3BP1 MUTATED                                0
  G3BP1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  G3BP1 MUTATED                                    0
  G3BP1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  G3BP1 MUTATED                              0                             1
  G3BP1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  G3BP1 MUTATED                                               0
  G3BP1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  G3BP1 MUTATED                              0
  G3BP1 WILD-TYPE                            9
D43V10, multiclass
                                                    clus
vv                                                   G3BP1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   G3BP1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
D43V12, continuous
[1] "Remove cluster labels:" "G3BP1 MUTATED"         
clus
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              2             255 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4415      TCGA-05-4417      TCGA-05-4424 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4433      TCGA-05-5420      TCGA-05-5423 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-35-4122      TCGA-35-4123 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-7271 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5644 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-5645      TCGA-44-6144      TCGA-44-6145      TCGA-44-6147 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-6148      TCGA-44-6774      TCGA-44-6775      TCGA-44-6776 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-6777      TCGA-44-6778      TCGA-44-6779      TCGA-44-7659 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-7660      TCGA-44-7661      TCGA-44-7662      TCGA-44-7667 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7670      TCGA-44-7672      TCGA-44-8117 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-8119      TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-A4SU      TCGA-49-4494      TCGA-49-4505      TCGA-53-7624 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-53-7626      TCGA-53-7813      TCGA-55-1592      TCGA-55-1595 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-5899      TCGA-55-6642      TCGA-55-6712      TCGA-55-6971 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7227      TCGA-55-7283      TCGA-55-7570      TCGA-55-7574 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7576      TCGA-55-7724      TCGA-55-7725      TCGA-55-7726 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7728      TCGA-55-7907      TCGA-55-7910      TCGA-55-7911 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8092      TCGA-55-8094 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8096      TCGA-55-8097      TCGA-55-8205      TCGA-55-8299 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8301      TCGA-55-8302      TCGA-55-8506      TCGA-55-8507 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8511      TCGA-55-8512      TCGA-55-8514      TCGA-55-8615 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X      TCGA-55-A48Y 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-A493      TCGA-55-A494      TCGA-62-8398      TCGA-64-1677 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-64-1681      TCGA-64-5774      TCGA-64-5775      TCGA-64-5778 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-64-5779      TCGA-64-5781      TCGA-69-7761      TCGA-69-7763 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-69-7764      TCGA-69-7765      TCGA-69-7974      TCGA-69-7979 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-69-8253      TCGA-69-8255      TCGA-69-A59K      TCGA-73-4659 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-73-4662      TCGA-73-4666      TCGA-73-4668      TCGA-73-4670 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-73-4675      TCGA-73-4676      TCGA-73-7498      TCGA-75-6214 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-75-7025      TCGA-75-7027      TCGA-75-7031      TCGA-78-7145 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7146      TCGA-78-7147      TCGA-78-7148      TCGA-78-7149 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7150      TCGA-78-7152      TCGA-78-7153      TCGA-78-7154 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7155      TCGA-78-7156      TCGA-78-7158      TCGA-78-7159 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7160      TCGA-78-7161      TCGA-78-7162      TCGA-78-7163 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7166      TCGA-78-7167      TCGA-78-7220      TCGA-78-7535 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7536      TCGA-78-7537      TCGA-78-7539      TCGA-78-7542 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7633      TCGA-78-8640      TCGA-78-8648      TCGA-78-8655 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-8660      TCGA-78-8662      TCGA-80-5607      TCGA-80-5608 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-6851      TCGA-86-7711      TCGA-86-7714 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-8054      TCGA-86-8055      TCGA-86-8056 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8073      TCGA-86-8074      TCGA-86-8281      TCGA-86-8358 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8669      TCGA-86-8673      TCGA-86-8674 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-A456      TCGA-91-6829      TCGA-91-6830      TCGA-91-6836 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-91-6840      TCGA-91-6849      TCGA-91-8499      TCGA-91-A4BC 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-8067      TCGA-93-A4JN 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043      TCGA-95-7562 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-95-7567      TCGA-95-7944      TCGA-95-7947      TCGA-95-7948 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP      TCGA-97-7546 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-7553      TCGA-97-7554      TCGA-97-7941      TCGA-97-8171 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-8172      TCGA-97-8174      TCGA-97-8176      TCGA-97-8179 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M2 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7      TCGA-99-7458 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-99-8025      TCGA-99-8028      TCGA-99-8032      TCGA-J2-8194 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MN-A4N4 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4T2 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8      TCGA-MP-A4T9 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE      TCGA-MP-A4TF 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK      TCGA-MP-A5C7 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  G3BP1 MUTATED     4   0   1   1
  G3BP1 WILD-TYPE 306  11   3  24
D43V13, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             1               3
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  G3BP1 MUTATED                                  0     0
  G3BP1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  G3BP1 MUTATED                           2     4
  G3BP1 WILD-TYPE                        27   373
D43V14, multiclass
                                  clus
vv                                 G3BP1 MUTATED G3BP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, binary
                 cls
clus                0   1
  G3BP1 MUTATED     1   5
  G3BP1 WILD-TYPE   5 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      1    5
  G3BP1 WILD-TYPE    5  344
                        clus
vv                       G3BP1 MUTATED G3BP1 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(44) Variable = TRERF1 MUTATION ANALYSIS
D44V1, survival
                  sevent
clus2                0   1
  TRERF1 MUTATED     8   9
  TRERF1 WILD-TYPE 294 146
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              17              440 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
               9              146 
$`TRERF1 MUTATED`
TCGA-05-4250 TCGA-05-5420 TCGA-44-7670 TCGA-49-4488 TCGA-55-7907 TCGA-55-8511 
        3.98        15.02        29.00        28.57         0.53         0.30 
TCGA-62-A46O TCGA-64-1677 TCGA-69-7978 TCGA-78-7145 TCGA-78-7155 TCGA-78-7220 
       47.80        20.65         4.41        27.16        38.50        26.53 
TCGA-78-8662 TCGA-93-8067 TCGA-95-8494 TCGA-J2-8194 TCGA-O1-A52J 
      110.50         6.12         2.76        23.80        59.11 

$`TRERF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        76.21        28.11        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36         0.26         0.49        17.72         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        56.81        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       39.09        50.33       163.10         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
      129.53        21.90        39.95       119.51        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29        41.82        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.68        15.65        27.29        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.57        24.30        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R 
        0.43        19.82 

  TRERF1 MUTATED TRERF1 WILD-TYPE 
             0.3              0.0 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
          110.50           238.29 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
          23.800           19.745 
[1] "0.3 - 110.5 (23.8)" "0.0 - 238.3 (19.7)"
[1] "hr=" "1.5"
D44V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TRERF1 MUTATED         0        2        6         3         2          4
  TRERF1 WILD-TYPE       4      121      126        44        64         66
                  vv
clus               STAGE IIIB STAGE IV
  TRERF1 MUTATED            0        1
  TRERF1 WILD-TYPE         11       24
D44V3, multiclass
            clus
vv           TRERF1 MUTATED TRERF1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                6              126
  STAGE IIA               3               44
  STAGE IIB               2               64
  STAGE IIIA              4               66
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRERF1 MUTATED     3  12   2   1
  TRERF1 WILD-TYPE 152 249  41  17
D44V4, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  T1              3              152
  T2             12              249
  T3              2               41
  T4              1               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
  TRERF1 MUTATED     9   6     3
  TRERF1 WILD-TYPE 298  83    69
D44V5, multiclass
       clus
vv      TRERF1 MUTATED TRERF1 WILD-TYPE
  N0                 9              298
  N1                 6               83
  N2+N3              3               69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     9   1
  TRERF1 WILD-TYPE 319  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      9    1
  TRERF1 WILD-TYPE  319   22
   clus
vv  TRERF1 MUTATED TRERF1 WILD-TYPE
  0              9              319
  1              1               22
[1] 2 2
[1] FALSE
D44V7, binary
                  cls
clus                 0   1
  TRERF1 MUTATED    12   6
  TRERF1 WILD-TYPE 247 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     12    6
  TRERF1 WILD-TYPE  247  215
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  FEMALE             12              247
  MALE                6              215
[1] 2 2
[1] FALSE
D44V8, binary
                  cls
clus                 0   1
  TRERF1 MUTATED    11   2
  TRERF1 WILD-TYPE 322  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     11    2
  TRERF1 WILD-TYPE  322   47
     clus
vv    TRERF1 MUTATED TRERF1 WILD-TYPE
  NO              11              322
  YES              2               47
[1] 2 2
[1] FALSE
D44V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TRERF1 MUTATED                            0                                 3
  TRERF1 WILD-TYPE                         18                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TRERF1 MUTATED                                                   15
  TRERF1 WILD-TYPE                                                280
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TRERF1 MUTATED                                            0
  TRERF1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TRERF1 MUTATED                                               0
  TRERF1 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  TRERF1 MUTATED                                0
  TRERF1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  TRERF1 MUTATED                                    0
  TRERF1 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TRERF1 MUTATED                              0                             0
  TRERF1 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TRERF1 MUTATED                                               0
  TRERF1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  TRERF1 MUTATED                              0
  TRERF1 WILD-TYPE                            9
D44V10, multiclass
                                                    clus
vv                                                   TRERF1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   TRERF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
D44V12, continuous
                  vv
clus                R0  R1  R2  RX
  TRERF1 MUTATED    10   1   1   1
  TRERF1 WILD-TYPE 300  10   3  24
D44V13, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  R0             10              300
  R1              1               10
  R2              1                3
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRERF1 MUTATED                                  0     1
  TRERF1 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRERF1 MUTATED                           0    14
  TRERF1 WILD-TYPE                        29   363
D44V14, multiclass
                                  clus
vv                                 TRERF1 MUTATED TRERF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        14              363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     1  11
  TRERF1 WILD-TYPE   5 338
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      1   11
  TRERF1 WILD-TYPE    5  338
                        clus
vv                       TRERF1 MUTATED TRERF1 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             11              338
[1] 2 2
[1] FALSE

Clustering(45) Variable = CACNA1F MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  CACNA1F MUTATED    18   8
  CACNA1F WILD-TYPE 284 147
  CACNA1F MUTATED CACNA1F WILD-TYPE 
               26               431 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
                8               147 
$`CACNA1F MUTATED`
TCGA-05-4402 TCGA-38-4631 TCGA-44-A4SS TCGA-49-4514 TCGA-49-6743 TCGA-50-5045 
        8.02        11.64        13.64        55.89        53.29        71.47 
TCGA-53-A4EZ TCGA-55-7281 TCGA-55-8203 TCGA-55-8301 TCGA-55-8511 TCGA-55-A48X 
       35.21         0.59        17.98         1.45         0.30        22.65 
TCGA-62-A46R TCGA-64-5778 TCGA-64-5815 TCGA-69-7979 TCGA-69-A59K TCGA-78-7147 
       56.71        42.90        28.47         2.93        17.16        19.27 
TCGA-78-7166 TCGA-78-7220 TCGA-91-8497 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7941 
        8.48        26.53        14.27        18.18        31.69         0.72 
TCGA-L9-A444 TCGA-MN-A4N4 
       10.09        38.63 

$`CACNA1F WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03        47.05        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       16.04        55.33        17.16        11.64        22.26        20.52 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       30.54        13.94        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1.74         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
        1.08         1.51         2.17        22.16        15.42         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
        0.95         0.36         0.26         0.49        17.72         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        2.17        16.93        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 
       87.98         2.04        28.41        51.25        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 
        4.41        12.56        14.01        13.45         4.24         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        6.90        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16         5.69        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.18        16.60         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP 
       15.68        15.65        27.29         2.76        21.40        19.89 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  CACNA1F MUTATED CACNA1F WILD-TYPE 
              0.3               0.0 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
            71.47            238.29 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
            18.08             19.82 
[1] "0.3 - 71.5 (18.1)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CACNA1F MUTATED         0       10        6         3         4          3
  CACNA1F WILD-TYPE       4      113      126        44        62         67
                   vv
clus                STAGE IIIB STAGE IV
  CACNA1F MUTATED            0        1
  CACNA1F WILD-TYPE         11       24
D45V3, multiclass
            clus
vv           CACNA1F MUTATED CACNA1F WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                10               113
  STAGE IB                 6               126
  STAGE IIA                3                44
  STAGE IIB                4                62
  STAGE IIIA               3                67
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CACNA1F MUTATED    11  15   1   0
  CACNA1F WILD-TYPE 144 246  42  18
D45V4, multiclass
    clus
vv   CACNA1F MUTATED CACNA1F WILD-TYPE
  T1              11               144
  T2              15               246
  T3               1                42
  T4               0                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
  CACNA1F MUTATED    16   7     3
  CACNA1F WILD-TYPE 291  82    69
D45V5, multiclass
       clus
vv      CACNA1F MUTATED CACNA1F WILD-TYPE
  N0                 16               291
  N1                  7                82
  N2+N3               3                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  CACNA1F MUTATED    17   1
  CACNA1F WILD-TYPE 311  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED     17    1
  CACNA1F WILD-TYPE  311   22
   clus
vv  CACNA1F MUTATED CACNA1F WILD-TYPE
  0              17               311
  1               1                22
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  CACNA1F MUTATED    20   7
  CACNA1F WILD-TYPE 239 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED     20    7
  CACNA1F WILD-TYPE  239  214
        clus
vv       CACNA1F MUTATED CACNA1F WILD-TYPE
  FEMALE              20               239
  MALE                 7               214
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  CACNA1F MUTATED    18   4
  CACNA1F WILD-TYPE 315  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED     18    4
  CACNA1F WILD-TYPE  315   45
     clus
vv    CACNA1F MUTATED CACNA1F WILD-TYPE
  NO               18               315
  YES               4                45
[1] 2 2
[1] FALSE
D45V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  CACNA1F MUTATED                            4
  CACNA1F WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  CACNA1F MUTATED                                   5
  CACNA1F WILD-TYPE                                96
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CACNA1F MUTATED                                                   14
  CACNA1F WILD-TYPE                                                281
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CACNA1F MUTATED                                            0
  CACNA1F WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CACNA1F MUTATED                                               1
  CACNA1F WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  CACNA1F MUTATED                                1
  CACNA1F WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  CACNA1F MUTATED                                    0
  CACNA1F WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CACNA1F MUTATED                              0                             1
  CACNA1F WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CACNA1F MUTATED                                               1
  CACNA1F WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  CACNA1F MUTATED                              0
  CACNA1F WILD-TYPE                            9
D45V10, multiclass
                                                    clus
vv                                                   CACNA1F MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              14
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   CACNA1F WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
D45V12, continuous
                   vv
clus                 R0  R1  R2  RX
  CACNA1F MUTATED    19   0   1   1
  CACNA1F WILD-TYPE 291  11   3  24
D45V13, multiclass
    clus
vv   CACNA1F MUTATED CACNA1F WILD-TYPE
  R0              19               291
  R1               0                11
  R2               1                 3
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNA1F MUTATED                                  0     0
  CACNA1F WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CACNA1F MUTATED                           2    23
  CACNA1F WILD-TYPE                        27   354
D45V14, multiclass
                                  clus
vv                                 CACNA1F MUTATED CACNA1F WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         23               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                   cls
clus                  0   1
  CACNA1F MUTATED     1  18
  CACNA1F WILD-TYPE   5 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED      1   18
  CACNA1F WILD-TYPE    5  331
                        clus
vv                       CACNA1F MUTATED CACNA1F WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              18               331
[1] 2 2
[1] FALSE

Clustering(46) Variable = NFE2L2 MUTATION ANALYSIS
D46V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED     6   7
  NFE2L2 WILD-TYPE 296 148
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              444 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               7              148 
$`NFE2L2 MUTATED`
TCGA-05-4422 TCGA-50-5930 TCGA-55-6975 TCGA-55-6982 TCGA-55-A48Y TCGA-62-8395 
       12.00         9.27         3.88        32.71        20.71        39.98 
TCGA-62-A471 TCGA-73-4658 TCGA-78-8660 TCGA-93-8067 TCGA-97-7941 TCGA-97-8174 
       40.96        52.60        10.55         6.12         0.72         5.39 
TCGA-J2-A4AD 
       18.08 

$`NFE2L2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 
       20.05         2.99        14.96         9.01        29.98        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       15.72        60.16        31.04        49.28         8.09        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 
        5.49         7.79         2.20        45.34        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 
        1.61         2.17        16.93        22.65        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
        4.57        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       39.25        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        17.16         2.01         6.90        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        50.33       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        9.57       104.19       238.29         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 
       50.24       232.18        39.75        77.59       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       22.45        17.46        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.59        18.67        17.92        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            0.72             0.00 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           52.60           238.29 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           12.00            19.82 
[1] "0.7 - 52.6 (12.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "2.1"
D46V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NFE2L2 MUTATED         0        2        3         2         5          1
  NFE2L2 WILD-TYPE       4      121      129        45        61         69
                  vv
clus               STAGE IIIB STAGE IV
  NFE2L2 MUTATED            0        0
  NFE2L2 WILD-TYPE         11       25
D46V3, multiclass
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                3              129
  STAGE IIA               2               45
  STAGE IIB               5               61
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NFE2L2 MUTATED     2  10   1   0
  NFE2L2 WILD-TYPE 153 251  42  18
D46V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1              2              153
  T2             10              251
  T3              1               42
  T4              0               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
  NFE2L2 MUTATED     8   4     1
  NFE2L2 WILD-TYPE 299  85    71
D46V5, multiclass
       clus
vv      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0                 8              299
  N1                 4               85
  N2+N3              1               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    10   0
  NFE2L2 WILD-TYPE 318  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     10    0
  NFE2L2 WILD-TYPE  318   23
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0             10              318
  1              0               23
[1] 2 2
[1] FALSE
D46V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     5   8
  NFE2L2 WILD-TYPE 254 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      5    8
  NFE2L2 WILD-TYPE  254  213
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              5              254
  MALE                8              213
[1] 2 2
[1] FALSE
D46V8, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     8   2
  NFE2L2 WILD-TYPE 325  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      8    2
  NFE2L2 WILD-TYPE  325   47
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               8              325
  YES              2               47
[1] 2 2
[1] FALSE
D46V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NFE2L2 MUTATED                            1                                 4
  NFE2L2 WILD-TYPE                         17                                97
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NFE2L2 MUTATED                                                    7
  NFE2L2 WILD-TYPE                                                288
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NFE2L2 MUTATED                                            0
  NFE2L2 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NFE2L2 MUTATED                                               0
  NFE2L2 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  NFE2L2 MUTATED                                0
  NFE2L2 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  NFE2L2 MUTATED                                    0
  NFE2L2 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NFE2L2 MUTATED                              0                             1
  NFE2L2 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NFE2L2 MUTATED                                               0
  NFE2L2 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  NFE2L2 MUTATED                              0
  NFE2L2 WILD-TYPE                            9
D46V10, multiclass
                                                    clus
vv                                                   NFE2L2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   NFE2L2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
D46V12, continuous
                  vv
clus                R0  R1  R2  RX
  NFE2L2 MUTATED     7   0   0   2
  NFE2L2 WILD-TYPE 303  11   4  23
D46V13, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  R0              7              303
  R1              0               11
  R2              0                4
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L2 MUTATED                                  0     1
  NFE2L2 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED                           0    10
  NFE2L2 WILD-TYPE                        29   367
D46V14, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        10              367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0  10
  NFE2L2 WILD-TYPE   6 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   10
  NFE2L2 WILD-TYPE    6  339
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10              339
[1] 2 2
[1] FALSE

Clustering(47) Variable = RPL5 MUTATION ANALYSIS
D47V1, survival
                sevent
clus2              0   1
  RPL5 MUTATED     5   2
  RPL5 WILD-TYPE 297 153
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            450 
  RPL5 MUTATED RPL5 WILD-TYPE 
             2            153 
$`RPL5 MUTATED`
TCGA-49-6742 TCGA-55-7994 TCGA-62-8395 TCGA-78-8662 TCGA-91-6849 TCGA-97-8177 
       16.04        19.82        39.98       110.50         1.15        16.41 
TCGA-NJ-A55R 
       19.82 

$`RPL5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94        35.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 
       15.81        20.19        19.99         4.57        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
      232.18        39.75        77.59        10.55        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 
       13.71        12.23        27.68         7.36        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.13         1.64        29.13         0.26         0.43        59.11 

  RPL5 MUTATED RPL5 WILD-TYPE 
          1.15           0.00 
  RPL5 MUTATED RPL5 WILD-TYPE 
        110.50         238.29 
  RPL5 MUTATED RPL5 WILD-TYPE 
         19.82          19.79 
[1] "1.1 - 110.5 (19.8)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.6"
D47V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RPL5 MUTATED         0        1        2         1         3          1
  RPL5 WILD-TYPE       4      122      130        46        63         69
                vv
clus             STAGE IIIB STAGE IV
  RPL5 MUTATED            0        0
  RPL5 WILD-TYPE         11       25
D47V3, multiclass
            clus
vv           RPL5 MUTATED RPL5 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              2            130
  STAGE IIA             1             46
  STAGE IIB             3             63
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RPL5 MUTATED     1   4   3   0
  RPL5 WILD-TYPE 154 257  40  18
D47V4, multiclass
    clus
vv   RPL5 MUTATED RPL5 WILD-TYPE
  T1            1            154
  T2            4            257
  T3            3             40
  T4            0             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
  RPL5 MUTATED     6   1     1
  RPL5 WILD-TYPE 301  88    71
D47V5, multiclass
       clus
vv      RPL5 MUTATED RPL5 WILD-TYPE
  N0               6            301
  N1               1             88
  N2+N3            1             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                cls
clus               0   1
  RPL5 MUTATED     5   0
  RPL5 WILD-TYPE 323  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      5    0
  RPL5 WILD-TYPE  323   23
   clus
vv  RPL5 MUTATED RPL5 WILD-TYPE
  0            5            323
  1            0             23
[1] 2 2
[1] FALSE
D47V7, binary
                cls
clus               0   1
  RPL5 MUTATED     4   4
  RPL5 WILD-TYPE 255 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      4    4
  RPL5 WILD-TYPE  255  217
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  FEMALE            4            255
  MALE              4            217
[1] 2 2
[1] FALSE
D47V8, binary
                cls
clus               0   1
  RPL5 MUTATED     7   0
  RPL5 WILD-TYPE 326  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      7    0
  RPL5 WILD-TYPE  326   49
     clus
vv    RPL5 MUTATED RPL5 WILD-TYPE
  NO             7            326
  YES            0             49
[1] 2 2
[1] FALSE
D47V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RPL5 MUTATED                            0                                 2
  RPL5 WILD-TYPE                         18                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RPL5 MUTATED                                                    5
  RPL5 WILD-TYPE                                                290
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RPL5 MUTATED                                            0
  RPL5 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RPL5 MUTATED                                               0
  RPL5 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  RPL5 MUTATED                                0
  RPL5 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  RPL5 MUTATED                                    0
  RPL5 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RPL5 MUTATED                              0                             0
  RPL5 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RPL5 MUTATED                                               0
  RPL5 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  RPL5 MUTATED                              1
  RPL5 WILD-TYPE                            8
D47V10, multiclass
                                                    clus
vv                                                   RPL5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  1
                                                    clus
vv                                                   RPL5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
D47V12, continuous
[1] "Remove cluster labels:" "RPL5 MUTATED"          
clus
  RPL5 MUTATED RPL5 WILD-TYPE 
             2            255 
    TCGA-05-4384     TCGA-05-4390     TCGA-05-4396     TCGA-05-4405 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-05-4410     TCGA-05-4415     TCGA-05-4417     TCGA-05-4424 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-05-4427     TCGA-05-4433     TCGA-05-5420     TCGA-05-5423 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-35-4122     TCGA-35-4123 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4625     TCGA-38-4626     TCGA-38-7271 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2656     TCGA-44-2657     TCGA-44-3396 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-4112     TCGA-44-5644 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-5645     TCGA-44-6144     TCGA-44-6145     TCGA-44-6147 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6774     TCGA-44-6775     TCGA-44-6776 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-6777     TCGA-44-6778     TCGA-44-6779     TCGA-44-7659 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-7660     TCGA-44-7661     TCGA-44-7662     TCGA-44-7667 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-7669     TCGA-44-7670     TCGA-44-7672     TCGA-44-8117 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-8119     TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47F     TCGA-44-A47G     TCGA-44-A4SS 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4494     TCGA-49-4505 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-1592     TCGA-55-1595     TCGA-55-5899     TCGA-55-6642 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-6712     TCGA-55-6971     TCGA-55-7227     TCGA-55-7283 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-7570     TCGA-55-7574     TCGA-55-7576     TCGA-55-7724 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7728     TCGA-55-7907 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7911     TCGA-55-7914     TCGA-55-8089 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8096     TCGA-55-8097 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8299     TCGA-55-8301     TCGA-55-8302 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8511     TCGA-55-8512 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8615     TCGA-55-8620     TCGA-55-8621 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-A48X     TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-A491     TCGA-55-A492     TCGA-55-A493     TCGA-55-A494 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-62-8398     TCGA-64-1677     TCGA-64-1681     TCGA-64-5774 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-64-5779     TCGA-64-5781 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-69-7761     TCGA-69-7763     TCGA-69-7764     TCGA-69-7765 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-7979     TCGA-69-8253     TCGA-69-8255 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-69-A59K     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4675     TCGA-73-4676 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-73-7498     TCGA-75-6214     TCGA-75-7025     TCGA-75-7027 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-75-7031     TCGA-78-7145     TCGA-78-7146     TCGA-78-7147 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7148     TCGA-78-7149     TCGA-78-7150     TCGA-78-7152 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7153     TCGA-78-7154     TCGA-78-7155     TCGA-78-7156 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7158     TCGA-78-7159     TCGA-78-7160     TCGA-78-7161 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7162     TCGA-78-7163     TCGA-78-7166     TCGA-78-7167 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7220     TCGA-78-7535     TCGA-78-7536     TCGA-78-7537 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7539     TCGA-78-7542     TCGA-78-7633     TCGA-78-8640 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-8648     TCGA-78-8655     TCGA-78-8660     TCGA-80-5607 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-80-5608     TCGA-83-5908     TCGA-86-6851     TCGA-86-7711 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7954     TCGA-86-8054     TCGA-86-8055 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8281 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8669     TCGA-86-8673 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-91-6829     TCGA-91-6830 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-91-6836     TCGA-91-6840     TCGA-91-8499     TCGA-91-A4BC 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-8067     TCGA-93-A4JN 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-93-A4JQ     TCGA-95-7043     TCGA-95-7562 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-95-7567     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-95-A4VP     TCGA-97-7546 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7941     TCGA-97-8171 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-8172     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-A4LX     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M2 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M5     TCGA-97-A4M7     TCGA-99-7458 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-99-8025     TCGA-99-8028     TCGA-99-8032     TCGA-J2-8194 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-J2-A4AD     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4T2 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T7     TCGA-MP-A4T8     TCGA-MP-A4T9 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TE     TCGA-MP-A4TF 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  RPL5 MUTATED     5   0   0   0
  RPL5 WILD-TYPE 305  11   4  25
D47V13, multiclass
    clus
vv   RPL5 MUTATED RPL5 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPL5 MUTATED                                  0     0
  RPL5 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RPL5 MUTATED                           1     5
  RPL5 WILD-TYPE                        28   372
D47V14, multiclass
                                  clus
vv                                 RPL5 MUTATED RPL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       5            372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V15, binary
                cls
clus               0   1
  RPL5 MUTATED     0   6
  RPL5 WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      0    6
  RPL5 WILD-TYPE    6  343
                        clus
vv                       RPL5 MUTATED RPL5 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(48) Variable = STRA8 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2               0   1
  STRA8 MUTATED     6   2
  STRA8 WILD-TYPE 296 153
  STRA8 MUTATED STRA8 WILD-TYPE 
              8             449 
  STRA8 MUTATED STRA8 WILD-TYPE 
              2             153 
$`STRA8 MUTATED`
TCGA-05-4382 TCGA-05-4397 TCGA-44-5643 TCGA-44-5644 TCGA-44-7670 TCGA-73-4668 
       19.96        24.03        33.30        28.37        29.00        15.35 
TCGA-78-7536 TCGA-86-8054 
        8.02        37.74 

$`STRA8 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.24        34.06        33.73        26.56        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       19.46        12.03         7.17        36.07        18.87        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        16.04 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
       53.29        55.33        17.16        11.64        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.09         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12         9.37        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94        35.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       51.25        28.47        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
        6.90        52.60        23.38        82.68        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53        31.20        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       38.04        20.55        32.78        19.89        35.24         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29        41.82        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  STRA8 MUTATED STRA8 WILD-TYPE 
           8.02            0.00 
  STRA8 MUTATED STRA8 WILD-TYPE 
          37.74          238.29 
  STRA8 MUTATED STRA8 WILD-TYPE 
          26.20           19.73 
[1] "8.0 - 37.7 (26.2)"  "0.0 - 238.3 (19.7)"
[1] "hr=" "1.2"
D48V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  STRA8 MUTATED         0        0        2         1         3          2
  STRA8 WILD-TYPE       4      123      130        46        63         68
                 vv
clus              STAGE IIIB STAGE IV
  STRA8 MUTATED            0        0
  STRA8 WILD-TYPE         11       25
D48V3, multiclass
            clus
vv           STRA8 MUTATED STRA8 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               2             130
  STAGE IIA              1              46
  STAGE IIB              3              63
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STRA8 MUTATED     1   7   0   0
  STRA8 WILD-TYPE 154 254  43  18
D48V4, multiclass
    clus
vv   STRA8 MUTATED STRA8 WILD-TYPE
  T1             1             154
  T2             7             254
  T3             0              43
  T4             0              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
  STRA8 MUTATED     2   4     2
  STRA8 WILD-TYPE 305  85    70
D48V5, multiclass
       clus
vv      STRA8 MUTATED STRA8 WILD-TYPE
  N0                2             305
  N1                4              85
  N2+N3             2              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                 cls
clus                0   1
  STRA8 MUTATED     7   0
  STRA8 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      7    0
  STRA8 WILD-TYPE  321   23
   clus
vv  STRA8 MUTATED STRA8 WILD-TYPE
  0             7             321
  1             0              23
[1] 2 2
[1] FALSE
D48V7, binary
                 cls
clus                0   1
  STRA8 MUTATED     3   5
  STRA8 WILD-TYPE 256 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      3    5
  STRA8 WILD-TYPE  256  216
        clus
vv       STRA8 MUTATED STRA8 WILD-TYPE
  FEMALE             3             256
  MALE               5             216
[1] 2 2
[1] FALSE
D48V8, binary
                 cls
clus                0   1
  STRA8 MUTATED     4   2
  STRA8 WILD-TYPE 329  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      4    2
  STRA8 WILD-TYPE  329   47
     clus
vv    STRA8 MUTATED STRA8 WILD-TYPE
  NO              4             329
  YES             2              47
[1] 2 2
[1] FALSE
D48V9, continuous
[1] "Remove cluster labels:" "STRA8 MUTATED"         
clus
  STRA8 MUTATED STRA8 WILD-TYPE 
              2             115 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-44-3396 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-6144      TCGA-44-6147 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-44-A47F      TCGA-49-4486 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-49-4494      TCGA-49-4505      TCGA-49-4506      TCGA-49-4510 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-49-6742      TCGA-49-6743      TCGA-49-6744      TCGA-53-7624 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-7283      TCGA-55-7573      TCGA-55-7725 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7914      TCGA-55-8089      TCGA-55-8096 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8208      TCGA-55-8507      TCGA-55-8508 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-8511      TCGA-55-8512      TCGA-55-8619      TCGA-55-8620 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-8621      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-69-7974      TCGA-69-8254 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4659      TCGA-73-4662 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-73-4666      TCGA-73-4670      TCGA-73-4676      TCGA-73-4677 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-6562      TCGA-86-6851      TCGA-86-7701      TCGA-86-7711 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7953      TCGA-86-7954 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-7955      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8280      TCGA-86-8281      TCGA-86-8358 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-91-6849      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567      TCGA-99-7458 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STRA8 MUTATED                            1                                 2
  STRA8 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STRA8 MUTATED                                                    4
  STRA8 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  STRA8 MUTATED                                            0
  STRA8 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  STRA8 MUTATED                                               0
  STRA8 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  STRA8 MUTATED                                0
  STRA8 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  STRA8 MUTATED                                    1
  STRA8 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  STRA8 MUTATED                              0                             0
  STRA8 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  STRA8 MUTATED                                               0
  STRA8 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  STRA8 MUTATED                              0
  STRA8 WILD-TYPE                            9
D48V10, multiclass
                                                    clus
vv                                                   STRA8 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   STRA8 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, continuous
D48V12, continuous
                 vv
clus               R0  R1  R2  RX
  STRA8 MUTATED     5   0   0   0
  STRA8 WILD-TYPE 305  11   4  25
D48V13, multiclass
    clus
vv   STRA8 MUTATED STRA8 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STRA8 MUTATED                                  1     0
  STRA8 WILD-TYPE                                0     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STRA8 MUTATED                           1     4
  STRA8 WILD-TYPE                        28   373
D48V14, multiclass
                                  clus
vv                                 STRA8 MUTATED STRA8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        4             373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                 cls
clus                0   1
  STRA8 MUTATED     1   4
  STRA8 WILD-TYPE   5 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      1    4
  STRA8 WILD-TYPE    5  345
                        clus
vv                       STRA8 MUTATED STRA8 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             4             345
[1] 2 2
[1] FALSE

Clustering(49) Variable = NLRP6 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  NLRP6 MUTATED     7   2
  NLRP6 WILD-TYPE 295 153
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              9             448 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2             153 
$`NLRP6 MUTATED`
TCGA-05-4420 TCGA-44-7660 TCGA-55-6642 TCGA-55-7907 TCGA-55-8094 TCGA-86-7714 
       29.98        19.46        32.65         0.53         0.13        20.55 
TCGA-97-A4M7 TCGA-99-8025 TCGA-MP-A4SV 
       20.68        34.85        86.14 

$`NLRP6 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
       35.21        23.05        48.62         2.86         0.07         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        5.06        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       51.25        28.47        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        6.90        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        38.04        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       26.50        29.46        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       20.52        17.75        20.84        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63         2.76        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  NLRP6 MUTATED NLRP6 WILD-TYPE 
           0.13            0.00 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          86.14          238.29 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
         20.680          19.745 
[1] "0.1 - 86.1 (20.7)"  "0.0 - 238.3 (19.7)"
[1] "hr=" "1.7"
D49V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NLRP6 MUTATED         0        1        5         1         0          2
  NLRP6 WILD-TYPE       4      122      127        46        66         68
                 vv
clus              STAGE IIIB STAGE IV
  NLRP6 MUTATED            0        1
  NLRP6 WILD-TYPE         11       24
D49V3, multiclass
            clus
vv           NLRP6 MUTATED NLRP6 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               5             127
  STAGE IIA              1              46
  STAGE IIB              0              66
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NLRP6 MUTATED     2   7   1   0
  NLRP6 WILD-TYPE 153 254  42  18
D49V4, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  T1             2             153
  T2             7             254
  T3             1              42
  T4             0              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
  NLRP6 MUTATED     7   1     2
  NLRP6 WILD-TYPE 300  88    70
D49V5, multiclass
       clus
vv      NLRP6 MUTATED NLRP6 WILD-TYPE
  N0                7             300
  N1                1              88
  N2+N3             2              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                 cls
clus                0   1
  NLRP6 MUTATED     6   1
  NLRP6 WILD-TYPE 322  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      6    1
  NLRP6 WILD-TYPE  322   22
   clus
vv  NLRP6 MUTATED NLRP6 WILD-TYPE
  0             6             322
  1             1              22
[1] 2 2
[1] FALSE
D49V7, binary
                 cls
clus                0   1
  NLRP6 MUTATED     3   7
  NLRP6 WILD-TYPE 256 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      3    7
  NLRP6 WILD-TYPE  256  214
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  FEMALE             3             256
  MALE               7             214
[1] 2 2
[1] FALSE
D49V8, binary
                 cls
clus                0   1
  NLRP6 MUTATED     7   0
  NLRP6 WILD-TYPE 326  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      7    0
  NLRP6 WILD-TYPE  326   49
     clus
vv    NLRP6 MUTATED NLRP6 WILD-TYPE
  NO              7             326
  YES             0              49
[1] 2 2
[1] FALSE
D49V9, continuous
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2             115 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-44-3396 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-6144      TCGA-44-6147 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-A47F      TCGA-49-4486      TCGA-49-4494 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4510      TCGA-49-6742 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-49-6743      TCGA-49-6744      TCGA-53-7624      TCGA-53-A4EZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7573      TCGA-55-7725      TCGA-55-7910 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8089      TCGA-55-8096      TCGA-55-8205 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-8621 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5775 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4676      TCGA-73-4677 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-6562      TCGA-86-6851      TCGA-86-7701      TCGA-86-7711 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7953      TCGA-86-7954      TCGA-86-7955 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8054      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8280      TCGA-86-8281      TCGA-86-8358 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-91-6849      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567      TCGA-99-7458 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NLRP6 MUTATED                            0                                 3
  NLRP6 WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NLRP6 MUTATED                                                    7
  NLRP6 WILD-TYPE                                                288
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NLRP6 MUTATED                                            0
  NLRP6 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NLRP6 MUTATED                                               0
  NLRP6 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  NLRP6 MUTATED                                0
  NLRP6 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  NLRP6 MUTATED                                    0
  NLRP6 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NLRP6 MUTATED                              0                             0
  NLRP6 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NLRP6 MUTATED                                               0
  NLRP6 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  NLRP6 MUTATED                              0
  NLRP6 WILD-TYPE                            9
D49V10, multiclass
                                                    clus
vv                                                   NLRP6 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             7
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   NLRP6 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             288
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
D49V12, continuous
                 vv
clus               R0  R1  R2  RX
  NLRP6 MUTATED     9   0   0   0
  NLRP6 WILD-TYPE 301  11   4  25
D49V13, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLRP6 MUTATED                                  0     0
  NLRP6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NLRP6 MUTATED                           2     5
  NLRP6 WILD-TYPE                        27   372
D49V14, multiclass
                                  clus
vv                                 NLRP6 MUTATED NLRP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   6
  NLRP6 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    6
  NLRP6 WILD-TYPE    6  343
                        clus
vv                       NLRP6 MUTATED NLRP6 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(50) Variable = FAM65C MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2                0   1
  FAM65C MUTATED    10   2
  FAM65C WILD-TYPE 292 153
  FAM65C MUTATED FAM65C WILD-TYPE 
              12              445 
  FAM65C MUTATED FAM65C WILD-TYPE 
               2              153 
$`FAM65C MUTATED`
TCGA-44-7667 TCGA-44-7670 TCGA-44-A47A TCGA-49-4486 TCGA-55-8506 TCGA-62-A46U 
       36.07        29.00        15.32        76.21         0.36        67.96 
TCGA-69-7978 TCGA-78-7163 TCGA-78-7220 TCGA-86-8073 TCGA-93-8067 TCGA-97-7547 
        4.41       238.29        26.53        24.33         6.12        64.60 

$`FAM65C WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
        7.17        18.87        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y 
       47.80        19.53        56.71        54.35        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 
       22.92         9.57       104.19         8.48        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
       17.46        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  FAM65C MUTATED FAM65C WILD-TYPE 
            0.36             0.00 
  FAM65C MUTATED FAM65C WILD-TYPE 
          238.29           232.18 
  FAM65C MUTATED FAM65C WILD-TYPE 
          27.765           19.730 
[1] "0.4 - 238.3 (27.8)" "0.0 - 232.2 (19.7)"
[1] "hr=" "3.7"
D50V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FAM65C MUTATED         0        1        5         1         4          3
  FAM65C WILD-TYPE       4      122      127        46        62         67
                  vv
clus               STAGE IIIB STAGE IV
  FAM65C MUTATED            0        0
  FAM65C WILD-TYPE         11       25
D50V3, multiclass
            clus
vv           FAM65C MUTATED FAM65C WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              122
  STAGE IB                5              127
  STAGE IIA               1               46
  STAGE IIB               4               62
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM65C MUTATED     2   9   3   0
  FAM65C WILD-TYPE 153 252  40  18
D50V4, multiclass
    clus
vv   FAM65C MUTATED FAM65C WILD-TYPE
  T1              2              153
  T2              9              252
  T3              3               40
  T4              0               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
  FAM65C MUTATED     8   3     3
  FAM65C WILD-TYPE 299  86    69
D50V5, multiclass
       clus
vv      FAM65C MUTATED FAM65C WILD-TYPE
  N0                 8              299
  N1                 3               86
  N2+N3              3               69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                  cls
clus                 0   1
  FAM65C MUTATED     8   0
  FAM65C WILD-TYPE 320  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED      8    0
  FAM65C WILD-TYPE  320   23
   clus
vv  FAM65C MUTATED FAM65C WILD-TYPE
  0              8              320
  1              0               23
[1] 2 2
[1] FALSE
D50V7, binary
                  cls
clus                 0   1
  FAM65C MUTATED     9   5
  FAM65C WILD-TYPE 250 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED      9    5
  FAM65C WILD-TYPE  250  216
        clus
vv       FAM65C MUTATED FAM65C WILD-TYPE
  FEMALE              9              250
  MALE                5              216
[1] 2 2
[1] FALSE
D50V8, binary
                  cls
clus                 0   1
  FAM65C MUTATED    12   1
  FAM65C WILD-TYPE 321  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED     12    1
  FAM65C WILD-TYPE  321   48
     clus
vv    FAM65C MUTATED FAM65C WILD-TYPE
  NO              12              321
  YES              1               48
[1] 2 2
[1] FALSE
D50V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FAM65C MUTATED                            0                                 3
  FAM65C WILD-TYPE                         18                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FAM65C MUTATED                                                    8
  FAM65C WILD-TYPE                                                287
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FAM65C MUTATED                                            0
  FAM65C WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FAM65C MUTATED                                               1
  FAM65C WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  FAM65C MUTATED                                0
  FAM65C WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  FAM65C MUTATED                                    0
  FAM65C WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FAM65C MUTATED                              0                             2
  FAM65C WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FAM65C MUTATED                                               0
  FAM65C WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  FAM65C MUTATED                              0
  FAM65C WILD-TYPE                            9
D50V10, multiclass
                                                    clus
vv                                                   FAM65C MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   FAM65C WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
D50V12, continuous
                  vv
clus                R0  R1  R2  RX
  FAM65C MUTATED     8   0   1   1
  FAM65C WILD-TYPE 302  11   3  24
D50V13, multiclass
    clus
vv   FAM65C MUTATED FAM65C WILD-TYPE
  R0              8              302
  R1              0               11
  R2              1                3
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM65C MUTATED                                  0     1
  FAM65C WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM65C MUTATED                           0    11
  FAM65C WILD-TYPE                        29   366
D50V14, multiclass
                                  clus
vv                                 FAM65C MUTATED FAM65C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                        11              366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V15, binary
                  cls
clus                 0   1
  FAM65C MUTATED     1   9
  FAM65C WILD-TYPE   5 340
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED      1    9
  FAM65C WILD-TYPE    5  340
                        clus
vv                       FAM65C MUTATED FAM65C WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              9              340
[1] 2 2
[1] FALSE

Clustering(51) Variable = WDR66 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  WDR66 MUTATED     8   5
  WDR66 WILD-TYPE 294 150
  WDR66 MUTATED WDR66 WILD-TYPE 
             13             444 
  WDR66 MUTATED WDR66 WILD-TYPE 
              5             150 
$`WDR66 MUTATED`
TCGA-05-4420 TCGA-35-5375 TCGA-53-7624 TCGA-55-A48X TCGA-62-8399 TCGA-67-3771 
       29.98         8.68        34.29        22.65        88.64        20.05 
TCGA-78-7155 TCGA-78-7536 TCGA-78-7539 TCGA-78-8662 TCGA-86-8056 TCGA-99-8025 
       38.50         8.02        26.01       110.50         4.57        34.85 
TCGA-O1-A52J 
       59.11 

$`WDR66 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         5.98        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.99         7.59        27.25        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61         2.17        16.93        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
       19.99         4.57        39.98        42.38        14.60        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       51.25        28.47        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        17.16         2.01         6.90 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        82.68        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.95       119.51        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
       26.53        31.20        53.33        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
      232.18        39.75        77.59        10.55        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 
       19.89        35.24        37.74         4.08        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 

  WDR66 MUTATED WDR66 WILD-TYPE 
           4.57            0.00 
  WDR66 MUTATED WDR66 WILD-TYPE 
         110.50          238.29 
  WDR66 MUTATED WDR66 WILD-TYPE 
         29.980          19.625 
[1] "4.6 - 110.5 (30.0)" "0.0 - 238.3 (19.6)"
[1] "hr=" "1.4"
D51V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  WDR66 MUTATED         0        2        4         2         0          5
  WDR66 WILD-TYPE       4      121      128        45        66         65
                 vv
clus              STAGE IIIB STAGE IV
  WDR66 MUTATED            0        1
  WDR66 WILD-TYPE         11       24
D51V3, multiclass
            clus
vv           WDR66 MUTATED WDR66 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               4             128
  STAGE IIA              2              45
  STAGE IIB              0              66
  STAGE IIIA             5              65
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR66 MUTATED     3   9   1   1
  WDR66 WILD-TYPE 152 252  42  17
D51V4, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  T1             3             152
  T2             9             252
  T3             1              42
  T4             1              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
  WDR66 MUTATED     9   1     4
  WDR66 WILD-TYPE 298  88    68
D51V5, multiclass
       clus
vv      WDR66 MUTATED WDR66 WILD-TYPE
  N0                9             298
  N1                1              88
  N2+N3             4              68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                 cls
clus                0   1
  WDR66 MUTATED    12   1
  WDR66 WILD-TYPE 316  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     12    1
  WDR66 WILD-TYPE  316   22
   clus
vv  WDR66 MUTATED WDR66 WILD-TYPE
  0            12             316
  1             1              22
[1] 2 2
[1] FALSE
D51V7, binary
                 cls
clus                0   1
  WDR66 MUTATED     8   6
  WDR66 WILD-TYPE 251 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED      8    6
  WDR66 WILD-TYPE  251  215
        clus
vv       WDR66 MUTATED WDR66 WILD-TYPE
  FEMALE             8             251
  MALE               6             215
[1] 2 2
[1] FALSE
D51V8, binary
                 cls
clus                0   1
  WDR66 MUTATED     9   1
  WDR66 WILD-TYPE 324  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED      9    1
  WDR66 WILD-TYPE  324   48
     clus
vv    WDR66 MUTATED WDR66 WILD-TYPE
  NO              9             324
  YES             1              48
[1] 2 2
[1] FALSE
D51V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  WDR66 MUTATED                            0                                 3
  WDR66 WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  WDR66 MUTATED                                                   10
  WDR66 WILD-TYPE                                                285
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  WDR66 MUTATED                                            0
  WDR66 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  WDR66 MUTATED                                               0
  WDR66 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  WDR66 MUTATED                                0
  WDR66 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  WDR66 MUTATED                                    0
  WDR66 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  WDR66 MUTATED                              0                             1
  WDR66 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  WDR66 MUTATED                                               0
  WDR66 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  WDR66 MUTATED                              0
  WDR66 WILD-TYPE                            9
D51V10, multiclass
                                                    clus
vv                                                   WDR66 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   WDR66 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
D51V12, continuous
                 vv
clus               R0  R1  R2  RX
  WDR66 MUTATED    13   0   0   0
  WDR66 WILD-TYPE 297  11   4  25
D51V13, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  R0            13             297
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR66 MUTATED                                  0     0
  WDR66 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR66 MUTATED                           2     9
  WDR66 WILD-TYPE                        27   368
D51V14, multiclass
                                  clus
vv                                 WDR66 MUTATED WDR66 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                 cls
clus                0   1
  WDR66 MUTATED     1   7
  WDR66 WILD-TYPE   5 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED      1    7
  WDR66 WILD-TYPE    5  342
                        clus
vv                       WDR66 MUTATED WDR66 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(52) Variable = RIT1 MUTATION ANALYSIS
D52V1, survival
                sevent
clus2              0   1
  RIT1 MUTATED     5   3
  RIT1 WILD-TYPE 297 152
  RIT1 MUTATED RIT1 WILD-TYPE 
             8            449 
  RIT1 MUTATED RIT1 WILD-TYPE 
             3            152 
$`RIT1 MUTATED`
TCGA-05-4384 TCGA-44-6779 TCGA-49-4514 TCGA-55-8094 TCGA-73-4666 TCGA-73-4675 
       14.01        16.44        55.89         0.13        26.30        30.31 
TCGA-86-A4JF TCGA-J2-A4AE 
       24.23        35.47 

$`RIT1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       61.28        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 
        2.01         6.90        52.60        23.38        82.68        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        4.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       26.50        29.46        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  RIT1 MUTATED RIT1 WILD-TYPE 
          0.13           0.00 
  RIT1 MUTATED RIT1 WILD-TYPE 
         55.89         238.29 
  RIT1 MUTATED RIT1 WILD-TYPE 
        25.265         19.760 
[1] "0.1 - 55.9 (25.3)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.1"
D52V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RIT1 MUTATED         0        2        0         0         2          2
  RIT1 WILD-TYPE       4      121      132        47        64         68
                vv
clus             STAGE IIIB STAGE IV
  RIT1 MUTATED            0        2
  RIT1 WILD-TYPE         11       23
D52V3, multiclass
            clus
vv           RIT1 MUTATED RIT1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              0            132
  STAGE IIA             0             47
  STAGE IIB             2             64
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RIT1 MUTATED     3   3   2   0
  RIT1 WILD-TYPE 152 258  41  18
D52V4, multiclass
    clus
vv   RIT1 MUTATED RIT1 WILD-TYPE
  T1            3            152
  T2            3            258
  T3            2             41
  T4            0             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
  RIT1 MUTATED     5   2     1
  RIT1 WILD-TYPE 302  87    71
D52V5, multiclass
       clus
vv      RIT1 MUTATED RIT1 WILD-TYPE
  N0               5            302
  N1               2             87
  N2+N3            1             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                cls
clus               0   1
  RIT1 MUTATED     4   2
  RIT1 WILD-TYPE 324  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      4    2
  RIT1 WILD-TYPE  324   21
   clus
vv  RIT1 MUTATED RIT1 WILD-TYPE
  0            4            324
  1            2             21
[1] 2 2
[1] FALSE
D52V7, binary
                cls
clus               0   1
  RIT1 MUTATED     4   4
  RIT1 WILD-TYPE 255 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      4    4
  RIT1 WILD-TYPE  255  217
        clus
vv       RIT1 MUTATED RIT1 WILD-TYPE
  FEMALE            4            255
  MALE              4            217
[1] 2 2
[1] FALSE
D52V8, binary
                cls
clus               0   1
  RIT1 MUTATED     5   2
  RIT1 WILD-TYPE 328  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      5    2
  RIT1 WILD-TYPE  328   47
     clus
vv    RIT1 MUTATED RIT1 WILD-TYPE
  NO             5            328
  YES            2             47
[1] 2 2
[1] FALSE
D52V9, continuous
[1] "Remove cluster labels:" "RIT1 MUTATED"          
clus
  RIT1 MUTATED RIT1 WILD-TYPE 
             2            115 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-44-3396 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-6144     TCGA-44-6147 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-44-A47F     TCGA-49-4486 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-49-4494     TCGA-49-4505     TCGA-49-4506     TCGA-49-4510 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-49-6742     TCGA-49-6743     TCGA-49-6744     TCGA-53-7624 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-53-A4EZ     TCGA-55-7283     TCGA-55-7573     TCGA-55-7725 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7914     TCGA-55-8089     TCGA-55-8096 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8208     TCGA-55-8507     TCGA-55-8508 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8619     TCGA-55-8620 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-8621     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-69-7974     TCGA-69-8254 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4659     TCGA-73-4662 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4676     TCGA-73-4677 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-6562     TCGA-86-6851     TCGA-86-7701     TCGA-86-7711 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7953     TCGA-86-7954 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-7955     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8280     TCGA-86-8281 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A456     TCGA-86-A4P7     TCGA-91-6829 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-91-6849     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-95-7567     TCGA-99-7458 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RIT1 MUTATED                            0                                 1
  RIT1 WILD-TYPE                         18                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RIT1 MUTATED                                                    6
  RIT1 WILD-TYPE                                                289
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RIT1 MUTATED                                            0
  RIT1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RIT1 MUTATED                                               0
  RIT1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  RIT1 MUTATED                                0
  RIT1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  RIT1 MUTATED                                    0
  RIT1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RIT1 MUTATED                              0                             1
  RIT1 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RIT1 MUTATED                                               0
  RIT1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  RIT1 MUTATED                              0
  RIT1 WILD-TYPE                            9
D52V10, multiclass
                                                    clus
vv                                                   RIT1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   RIT1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
D52V12, continuous
                vv
clus              R0  R1  R2  RX
  RIT1 MUTATED     5   0   0   2
  RIT1 WILD-TYPE 305  11   4  23
D52V13, multiclass
    clus
vv   RIT1 MUTATED RIT1 WILD-TYPE
  R0            5            305
  R1            0             11
  R2            0              4
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIT1 MUTATED                                  0     0
  RIT1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RIT1 MUTATED                           0     7
  RIT1 WILD-TYPE                        29   370
D52V14, multiclass
                                  clus
vv                                 RIT1 MUTATED RIT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, binary
                cls
clus               0   1
  RIT1 MUTATED     0   5
  RIT1 WILD-TYPE   6 344
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      0    5
  RIT1 WILD-TYPE    6  344
                        clus
vv                       RIT1 MUTATED RIT1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            344
[1] 2 2
[1] FALSE

Clustering(53) Variable = TGFBR3 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2                0   1
  TGFBR3 MUTATED    10   4
  TGFBR3 WILD-TYPE 292 151
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
              14              443 
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
               4              151 
$`TGFBR3 MUTATED`
TCGA-44-2656 TCGA-44-7662 TCGA-55-8089 TCGA-55-8205 TCGA-55-8615 TCGA-62-A46O 
       46.98         7.17         3.29         1.08         0.49        47.80 
TCGA-78-7220 TCGA-78-7536 TCGA-83-5908 TCGA-95-7043 TCGA-99-7458 TCGA-99-8025 
       26.53         8.02        27.09        16.54        24.56        34.85 
TCGA-L4-A4E5 TCGA-L9-A444 
       19.00        10.09 

$`TGFBR3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 
       61.28        16.44        22.72        19.46        12.03        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
        0.10         4.80         6.64        17.62         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        17.16         2.01         6.90 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        82.68        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       88.14        31.20        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29        41.82         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       20.68        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 
       18.08        35.47        32.48        14.30         6.35        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
            0.49             0.00 
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
           47.80           238.29 
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
           17.77            19.82 
[1] "0.5 - 47.8 (17.8)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.1"
D53V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TGFBR3 MUTATED         1        4        3         0         1          5
  TGFBR3 WILD-TYPE       3      119      129        47        65         65
                  vv
clus               STAGE IIIB STAGE IV
  TGFBR3 MUTATED            0        0
  TGFBR3 WILD-TYPE         11       25
D53V3, multiclass
            clus
vv           TGFBR3 MUTATED TGFBR3 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                4              119
  STAGE IB                3              129
  STAGE IIA               0               47
  STAGE IIB               1               65
  STAGE IIIA              5               65
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TGFBR3 MUTATED     5   6   2   1
  TGFBR3 WILD-TYPE 150 255  41  17
D53V4, multiclass
    clus
vv   TGFBR3 MUTATED TGFBR3 WILD-TYPE
  T1              5              150
  T2              6              255
  T3              2               41
  T4              1               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
  TGFBR3 MUTATED    10   0     4
  TGFBR3 WILD-TYPE 297  89    68
D53V5, multiclass
       clus
vv      TGFBR3 MUTATED TGFBR3 WILD-TYPE
  N0                10              297
  N1                 0               89
  N2+N3              4               68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                  cls
clus                 0   1
  TGFBR3 MUTATED    10   0
  TGFBR3 WILD-TYPE 318  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR3 MUTATED     10    0
  TGFBR3 WILD-TYPE  318   23
   clus
vv  TGFBR3 MUTATED TGFBR3 WILD-TYPE
  0             10              318
  1              0               23
[1] 2 2
[1] FALSE
D53V7, binary
                  cls
clus                 0   1
  TGFBR3 MUTATED     9   5
  TGFBR3 WILD-TYPE 250 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR3 MUTATED      9    5
  TGFBR3 WILD-TYPE  250  216
        clus
vv       TGFBR3 MUTATED TGFBR3 WILD-TYPE
  FEMALE              9              250
  MALE                5              216
[1] 2 2
[1] FALSE
D53V8, binary
                  cls
clus                 0   1
  TGFBR3 MUTATED     9   2
  TGFBR3 WILD-TYPE 324  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR3 MUTATED      9    2
  TGFBR3 WILD-TYPE  324   47
     clus
vv    TGFBR3 MUTATED TGFBR3 WILD-TYPE
  NO               9              324
  YES              2               47
[1] 2 2
[1] FALSE
D53V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TGFBR3 MUTATED                            0                                 2
  TGFBR3 WILD-TYPE                         18                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TGFBR3 MUTATED                                                   11
  TGFBR3 WILD-TYPE                                                284
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TGFBR3 MUTATED                                            0
  TGFBR3 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TGFBR3 MUTATED                                               1
  TGFBR3 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  TGFBR3 MUTATED                                0
  TGFBR3 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  TGFBR3 MUTATED                                    0
  TGFBR3 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TGFBR3 MUTATED                              0                             0
  TGFBR3 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TGFBR3 MUTATED                                               0
  TGFBR3 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  TGFBR3 MUTATED                              0
  TGFBR3 WILD-TYPE                            9
D53V10, multiclass
                                                    clus
vv                                                   TGFBR3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   TGFBR3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
D53V12, continuous
                  vv
clus                R0  R1  R2  RX
  TGFBR3 MUTATED    11   0   0   0
  TGFBR3 WILD-TYPE 299  11   4  25
D53V13, multiclass
    clus
vv   TGFBR3 MUTATED TGFBR3 WILD-TYPE
  R0             11              299
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGFBR3 MUTATED                                  0     0
  TGFBR3 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TGFBR3 MUTATED                           1    13
  TGFBR3 WILD-TYPE                        28   364
D53V14, multiclass
                                  clus
vv                                 TGFBR3 MUTATED TGFBR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        13              364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V15, binary
                  cls
clus                 0   1
  TGFBR3 MUTATED     0  12
  TGFBR3 WILD-TYPE   6 337
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR3 MUTATED      0   12
  TGFBR3 WILD-TYPE    6  337
                        clus
vv                       TGFBR3 MUTATED TGFBR3 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             12              337
[1] 2 2
[1] FALSE

Clustering(54) Variable = CXCR7 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2               0   1
  CXCR7 MUTATED     7   1
  CXCR7 WILD-TYPE 295 154
  CXCR7 MUTATED CXCR7 WILD-TYPE 
              8             449 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
              1             154 
$`CXCR7 MUTATED`
TCGA-44-8119 TCGA-55-8089 TCGA-55-8301 TCGA-67-4679 TCGA-78-7155 TCGA-91-6831 
        3.25         3.29         1.45        14.73        38.50        10.19 
TCGA-91-7771 TCGA-95-7039 
       16.18        41.82 

$`CXCR7 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94        35.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.04         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       50.33       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
      129.53        21.90        39.95       119.51        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36         1.97         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  CXCR7 MUTATED CXCR7 WILD-TYPE 
           1.45            0.00 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
          41.82          238.29 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
          12.46           19.82 
[1] "1.4 - 41.8 (12.5)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.7"
D54V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CXCR7 MUTATED         0        1        4         0         4          0
  CXCR7 WILD-TYPE       4      122      128        47        62         70
                 vv
clus              STAGE IIIB STAGE IV
  CXCR7 MUTATED            0        0
  CXCR7 WILD-TYPE         11       25
D54V3, multiclass
            clus
vv           CXCR7 MUTATED CXCR7 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               4             128
  STAGE IIA              0              47
  STAGE IIB              4              62
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CXCR7 MUTATED     1   5   4   0
  CXCR7 WILD-TYPE 154 256  39  18
D54V4, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  T1             1             154
  T2             5             256
  T3             4              39
  T4             0              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
  CXCR7 MUTATED     9   1     0
  CXCR7 WILD-TYPE 298  88    72
D54V5, multiclass
       clus
vv      CXCR7 MUTATED CXCR7 WILD-TYPE
  N0                9             298
  N1                1              88
  N2+N3             0              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                 cls
clus                0   1
  CXCR7 MUTATED     6   0
  CXCR7 WILD-TYPE 322  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED      6    0
  CXCR7 WILD-TYPE  322   23
   clus
vv  CXCR7 MUTATED CXCR7 WILD-TYPE
  0             6             322
  1             0              23
[1] 2 2
[1] FALSE
D54V7, binary
                 cls
clus                0   1
  CXCR7 MUTATED     1   9
  CXCR7 WILD-TYPE 258 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED      1    9
  CXCR7 WILD-TYPE  258  212
        clus
vv       CXCR7 MUTATED CXCR7 WILD-TYPE
  FEMALE             1             258
  MALE               9             212
[1] 2 2
[1] FALSE
D54V8, binary
                 cls
clus                0   1
  CXCR7 MUTATED     5   0
  CXCR7 WILD-TYPE 328  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED      5    0
  CXCR7 WILD-TYPE  328   49
     clus
vv    CXCR7 MUTATED CXCR7 WILD-TYPE
  NO              5             328
  YES             0              49
[1] 2 2
[1] FALSE
D54V9, continuous
[1] "Remove cluster labels:" "CXCR7 MUTATED"         
clus
  CXCR7 MUTATED CXCR7 WILD-TYPE 
              1             116 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-44-3396 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-6144      TCGA-44-6147 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-44-A47F      TCGA-49-4486 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-49-4494      TCGA-49-4505      TCGA-49-4506      TCGA-49-4510 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-49-6742      TCGA-49-6743      TCGA-49-6744      TCGA-53-7624 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-7283      TCGA-55-7573      TCGA-55-7725 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7914      TCGA-55-8096      TCGA-55-8205 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-8621 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5775 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4676      TCGA-73-4677 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-6562      TCGA-86-6851      TCGA-86-7701      TCGA-86-7711 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7953      TCGA-86-7954 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-7955      TCGA-86-8054      TCGA-86-8055      TCGA-86-8056 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-8073      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8280      TCGA-86-8281 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-91-6829      TCGA-91-6849      TCGA-93-7347      TCGA-93-7348 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-99-7458      TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CXCR7 MUTATED                            0                                 1
  CXCR7 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CXCR7 MUTATED                                                    9
  CXCR7 WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CXCR7 MUTATED                                            0
  CXCR7 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CXCR7 MUTATED                                               0
  CXCR7 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CXCR7 MUTATED                                0
  CXCR7 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CXCR7 MUTATED                                    0
  CXCR7 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CXCR7 MUTATED                              0                             0
  CXCR7 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CXCR7 MUTATED                                               0
  CXCR7 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CXCR7 MUTATED                              0
  CXCR7 WILD-TYPE                            9
D54V10, multiclass
                                                    clus
vv                                                   CXCR7 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CXCR7 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
D54V12, continuous
                 vv
clus               R0  R1  R2  RX
  CXCR7 MUTATED     5   0   0   1
  CXCR7 WILD-TYPE 305  11   4  24
D54V13, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CXCR7 MUTATED                                  0     0
  CXCR7 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CXCR7 MUTATED                           0     8
  CXCR7 WILD-TYPE                        29   369
D54V14, multiclass
                                  clus
vv                                 CXCR7 MUTATED CXCR7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        8             369
[1] 4 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
  CXCR7 MUTATED     0   7
  CXCR7 WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED      0    7
  CXCR7 WILD-TYPE    6  342
                        clus
vv                       CXCR7 MUTATED CXCR7 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             342
[1] 2 2
[1] FALSE

Clustering(55) Variable = GAN MUTATION ANALYSIS
D55V1, survival
               sevent
clus2             0   1
  GAN MUTATED     4   6
  GAN WILD-TYPE 298 149
  GAN MUTATED GAN WILD-TYPE 
           10           447 
  GAN MUTATED GAN WILD-TYPE 
            6           149 
$`GAN MUTATED`
TCGA-05-4249 TCGA-05-4396 TCGA-44-3918 TCGA-49-4494 TCGA-53-7626 TCGA-55-7574 
       50.07         9.96        34.06        35.54        30.54         3.12 
TCGA-62-A46O TCGA-78-7150 TCGA-91-6830 TCGA-MP-A4TK 
       47.80        21.90         1.97        19.13 

$`GAN WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 
       13.45        76.21        28.11        28.57        12.66        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       27.25        34.29        13.94        35.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.20         0.13         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       39.98        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        20.58       129.53        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        9.57       104.19       238.29         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 
       24.23        13.64        26.47        10.62        41.36        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
       10.09        29.46        11.05        24.36        14.10        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  GAN MUTATED GAN WILD-TYPE 
         1.97          0.00 
  GAN MUTATED GAN WILD-TYPE 
        50.07        238.29 
  GAN MUTATED GAN WILD-TYPE 
        26.22         19.76 
[1] "2.0 - 50.1 (26.2)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.7"
D55V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  GAN MUTATED         0        1        3         2         2          1
  GAN WILD-TYPE       4      122      129        45        64         69
               vv
clus            STAGE IIIB STAGE IV
  GAN MUTATED            1        0
  GAN WILD-TYPE         10       25
D55V3, multiclass
            clus
vv           GAN MUTATED GAN WILD-TYPE
  STAGE I              0             4
  STAGE IA             1           122
  STAGE IB             3           129
  STAGE IIA            2            45
  STAGE IIB            2            64
  STAGE IIIA           1            69
  STAGE IIIB           1            10
  STAGE IV             0            25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  GAN MUTATED     3   5   1   1
  GAN WILD-TYPE 152 256  42  17
D55V4, multiclass
    clus
vv   GAN MUTATED GAN WILD-TYPE
  T1           3           152
  T2           5           256
  T3           1            42
  T4           1            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
  GAN MUTATED     4   5     1
  GAN WILD-TYPE 303  84    71
D55V5, multiclass
       clus
vv      GAN MUTATED GAN WILD-TYPE
  N0              4           303
  N1              5            84
  N2+N3           1            71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
               cls
clus              0   1
  GAN MUTATED     8   0
  GAN WILD-TYPE 320  23
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      8    0
  GAN WILD-TYPE  320   23
   clus
vv  GAN MUTATED GAN WILD-TYPE
  0           8           320
  1           0            23
[1] 2 2
[1] FALSE
D55V7, binary
               cls
clus              0   1
  GAN MUTATED     6   4
  GAN WILD-TYPE 253 217
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      6    4
  GAN WILD-TYPE  253  217
        clus
vv       GAN MUTATED GAN WILD-TYPE
  FEMALE           6           253
  MALE             4           217
[1] 2 2
[1] FALSE
D55V8, binary
               cls
clus              0   1
  GAN MUTATED     7   0
  GAN WILD-TYPE 326  49
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      7    0
  GAN WILD-TYPE  326   49
     clus
vv    GAN MUTATED GAN WILD-TYPE
  NO            7           326
  YES           0            49
[1] 2 2
[1] FALSE
D55V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GAN MUTATED                            0                                 1
  GAN WILD-TYPE                         18                               100
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GAN MUTATED                                                    9
  GAN WILD-TYPE                                                286
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  GAN MUTATED                                            0
  GAN WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  GAN MUTATED                                               0
  GAN WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  GAN MUTATED                                0
  GAN WILD-TYPE                              2
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  GAN MUTATED                                    0                            0
  GAN WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  GAN MUTATED                               0
  GAN WILD-TYPE                            22
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  GAN MUTATED                                               0
  GAN WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  GAN MUTATED                              0
  GAN WILD-TYPE                            9
D55V10, multiclass
                                                    clus
vv                                                   GAN MUTATED GAN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   0            18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            1           100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           9           286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               0             2
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                0            22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
D55V12, continuous
               vv
clus             R0  R1  R2  RX
  GAN MUTATED     8   1   0   0
  GAN WILD-TYPE 302  10   4  25
D55V13, multiclass
    clus
vv   GAN MUTATED GAN WILD-TYPE
  R0           8           302
  R1           1            10
  R2           0             4
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAN MUTATED                                  0     0
  GAN WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  GAN MUTATED                           0     7
  GAN WILD-TYPE                        29   370
D55V14, multiclass
                                  clus
vv                                 GAN MUTATED GAN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  0            29
  WHITE                                      7           370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V15, binary
               cls
clus              0   1
  GAN MUTATED     0   6
  GAN WILD-TYPE   6 343
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      0    6
  GAN WILD-TYPE    6  343
                        clus
vv                       GAN MUTATED GAN WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           6           343
[1] 2 2
[1] FALSE

Clustering(56) Variable = TMEM49 MUTATION ANALYSIS
D56V1, survival
                  sevent
clus2                0   1
  TMEM49 MUTATED     2   3
  TMEM49 WILD-TYPE 300 152
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               5              452 
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               3              152 
$`TMEM49 MUTATED`
TCGA-50-5933 TCGA-50-8459 TCGA-53-7626 TCGA-69-7974 TCGA-MP-A4T4 
       78.67         7.59        30.54         6.05        86.04 

$`TMEM49 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.33        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        9.27        14.27        40.60        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
       10.13        36.99        27.25        34.29        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
        6.12        22.68        13.61         5.42         7.56         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       50.33       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        49.35        37.35        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  TMEM49 MUTATED TMEM49 WILD-TYPE 
            6.05             0.00 
  TMEM49 MUTATED TMEM49 WILD-TYPE 
           86.04           238.29 
  TMEM49 MUTATED TMEM49 WILD-TYPE 
           30.54            19.79 
[1] "6.0 - 86.0 (30.5)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1"  
D56V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TMEM49 MUTATED         0        0        0         1         2          1
  TMEM49 WILD-TYPE       4      123      132        46        64         69
                  vv
clus               STAGE IIIB STAGE IV
  TMEM49 MUTATED            1        0
  TMEM49 WILD-TYPE         10       25
D56V3, multiclass
            clus
vv           TMEM49 MUTATED TMEM49 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0              123
  STAGE IB                0              132
  STAGE IIA               1               46
  STAGE IIB               2               64
  STAGE IIIA              1               69
  STAGE IIIB              1               10
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEM49 MUTATED     1   2   1   1
  TMEM49 WILD-TYPE 154 259  42  17
D56V4, multiclass
    clus
vv   TMEM49 MUTATED TMEM49 WILD-TYPE
  T1              1              154
  T2              2              259
  T3              1               42
  T4              1               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
  TMEM49 MUTATED     1   2     2
  TMEM49 WILD-TYPE 306  87    70
D56V5, multiclass
       clus
vv      TMEM49 MUTATED TMEM49 WILD-TYPE
  N0                 1              306
  N1                 2               87
  N2+N3              2               70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                  cls
clus                 0   1
  TMEM49 MUTATED     4   0
  TMEM49 WILD-TYPE 324  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM49 MUTATED      4    0
  TMEM49 WILD-TYPE  324   23
   clus
vv  TMEM49 MUTATED TMEM49 WILD-TYPE
  0              4              324
  1              0               23
[1] 2 2
[1] FALSE
D56V7, binary
                  cls
clus                 0   1
  TMEM49 MUTATED     3   2
  TMEM49 WILD-TYPE 256 219
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM49 MUTATED      3    2
  TMEM49 WILD-TYPE  256  219
        clus
vv       TMEM49 MUTATED TMEM49 WILD-TYPE
  FEMALE              3              256
  MALE                2              219
[1] 2 2
[1] FALSE
D56V8, binary
                  cls
clus                 0   1
  TMEM49 MUTATED     3   2
  TMEM49 WILD-TYPE 330  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM49 MUTATED      3    2
  TMEM49 WILD-TYPE  330   47
     clus
vv    TMEM49 MUTATED TMEM49 WILD-TYPE
  NO               3              330
  YES              2               47
[1] 2 2
[1] FALSE
D56V9, continuous
[1] "Remove cluster labels:" "TMEM49 MUTATED"        
clus
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               1              116 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-44-3396 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-3918       TCGA-44-4112       TCGA-44-6144       TCGA-44-6147 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-6775       TCGA-44-7660       TCGA-44-A47F       TCGA-49-4486 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-4494       TCGA-49-4505       TCGA-49-4506       TCGA-49-4510 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-6742       TCGA-49-6743       TCGA-49-6744       TCGA-53-7624 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-53-A4EZ       TCGA-55-7283       TCGA-55-7573       TCGA-55-7725 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7910       TCGA-55-7914       TCGA-55-8089       TCGA-55-8096 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8205       TCGA-55-8208       TCGA-55-8507       TCGA-55-8508 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8511       TCGA-55-8512       TCGA-55-8619       TCGA-55-8620 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8621       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-A492       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-64-5775       TCGA-64-5778       TCGA-69-8254       TCGA-71-6725 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       TCGA-73-4662       TCGA-73-4666 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4670       TCGA-73-4676       TCGA-73-4677 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-83-5908 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-6562       TCGA-86-6851       TCGA-86-7701       TCGA-86-7711 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7953       TCGA-86-7954 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-7955       TCGA-86-8054       TCGA-86-8055       TCGA-86-8056 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8073       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8280       TCGA-86-8281 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8668       TCGA-86-8669 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8671       TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-91-6829       TCGA-91-6849       TCGA-93-7347       TCGA-93-7348 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-95-7567 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-99-7458       TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TMEM49 MUTATED                            0                                 1
  TMEM49 WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TMEM49 MUTATED                                                    3
  TMEM49 WILD-TYPE                                                292
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TMEM49 MUTATED                                            0
  TMEM49 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TMEM49 MUTATED                                               0
  TMEM49 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  TMEM49 MUTATED                                0
  TMEM49 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  TMEM49 MUTATED                                    0
  TMEM49 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TMEM49 MUTATED                              0                             0
  TMEM49 WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TMEM49 MUTATED                                               0
  TMEM49 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  TMEM49 MUTATED                              1
  TMEM49 WILD-TYPE                            8
D56V10, multiclass
                                                    clus
vv                                                   TMEM49 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    1
                                                    clus
vv                                                   TMEM49 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
D56V12, continuous
                  vv
clus                R0  R1  R2  RX
  TMEM49 MUTATED     2   0   0   0
  TMEM49 WILD-TYPE 308  11   4  25
D56V13, multiclass
[1] "Remove cluster labels:" "TMEM49 MUTATED"        
clus
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               2              348 
      TCGA-05-4244       TCGA-05-4249       TCGA-05-4250       TCGA-05-4382 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4384       TCGA-05-4389       TCGA-05-4390       TCGA-05-4395 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4396       TCGA-05-4397       TCGA-05-4398       TCGA-05-4402 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4403       TCGA-05-4405       TCGA-05-4410       TCGA-05-4415 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4417       TCGA-05-4418       TCGA-05-4420       TCGA-05-4422 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4424       TCGA-05-4425       TCGA-05-4426       TCGA-05-4427 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4430       TCGA-05-4432       TCGA-05-4433       TCGA-05-4434 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-5420       TCGA-05-5423       TCGA-05-5425       TCGA-05-5428 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-5429       TCGA-05-5715       TCGA-35-4122       TCGA-35-4123 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-35-5375       TCGA-38-4625       TCGA-38-4626       TCGA-38-4627 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-38-4628       TCGA-38-4629       TCGA-38-4630       TCGA-38-4631 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-38-4632       TCGA-38-6178       TCGA-38-7271       TCGA-38-A44F 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-2657       TCGA-44-2661       TCGA-44-2665       TCGA-44-3396 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-3398       TCGA-44-3918       TCGA-44-3919       TCGA-44-4112 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-6144       TCGA-44-6148       TCGA-44-6775       TCGA-44-A479 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-A47A       TCGA-44-A47B       TCGA-44-A47G       TCGA-44-A4SU 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4487       TCGA-49-4488       TCGA-49-4494 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-4501       TCGA-49-4505       TCGA-49-4506       TCGA-49-4507 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-4510       TCGA-49-4512       TCGA-49-4514       TCGA-49-6742 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-6744       TCGA-49-6761       TCGA-49-6767       TCGA-50-5051 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-50-5055       TCGA-50-5066       TCGA-50-5931       TCGA-50-5942 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-50-5944       TCGA-50-6593       TCGA-50-6597       TCGA-50-6673 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-50-8460       TCGA-53-7624       TCGA-53-A4EZ       TCGA-55-1592 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-5899       TCGA-55-6642       TCGA-55-6970       TCGA-55-6971 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-6972       TCGA-55-6980       TCGA-55-6981       TCGA-55-6983 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-6985       TCGA-55-7281       TCGA-55-7284       TCGA-55-7570 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7574       TCGA-55-7576       TCGA-55-7724       TCGA-55-7725 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7726       TCGA-55-7727       TCGA-55-7728       TCGA-55-7815 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7903       TCGA-55-7907       TCGA-55-7910       TCGA-55-7911 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-7994       TCGA-55-7995       TCGA-55-8085 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8087       TCGA-55-8089       TCGA-55-8090       TCGA-55-8091 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8092       TCGA-55-8094       TCGA-55-8097       TCGA-55-8203 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8204       TCGA-55-8205       TCGA-55-8206       TCGA-55-8207 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8208       TCGA-55-8299       TCGA-55-8301       TCGA-55-8302 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8505       TCGA-55-8506       TCGA-55-8507       TCGA-55-8508 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8510       TCGA-55-8511       TCGA-55-8512       TCGA-55-8513 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8514       TCGA-55-8614       TCGA-55-8615       TCGA-55-8616 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8620       TCGA-55-8621       TCGA-55-A48X 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-A492       TCGA-55-A493       TCGA-55-A494       TCGA-55-A4DF 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-A4DG       TCGA-62-8394       TCGA-62-8395       TCGA-62-8397 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-8398       TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-A472       TCGA-64-1676       TCGA-64-1677       TCGA-64-1679 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-64-1681       TCGA-64-5774       TCGA-64-5775       TCGA-64-5778 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-64-5779       TCGA-64-5781       TCGA-64-5815       TCGA-67-3771 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-67-3773       TCGA-67-4679       TCGA-67-6215       TCGA-67-6216 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-67-6217       TCGA-71-6725       TCGA-71-8520       TCGA-73-4658 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-73-4670       TCGA-73-4675       TCGA-73-4676       TCGA-73-4677 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-73-7498       TCGA-73-7499       TCGA-75-5122       TCGA-75-5125 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-75-5126       TCGA-75-5146       TCGA-75-5147       TCGA-75-6203 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-75-6205       TCGA-75-6206       TCGA-75-6207       TCGA-75-6211 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-75-6212       TCGA-75-6214       TCGA-75-7025       TCGA-75-7027 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-75-7030       TCGA-75-7031       TCGA-78-7143       TCGA-78-7145 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-7146       TCGA-78-7147       TCGA-78-7148       TCGA-78-7149 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-7150       TCGA-78-7152       TCGA-78-7153       TCGA-78-7154 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-7155       TCGA-78-7156       TCGA-78-7158       TCGA-78-7159 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-7160       TCGA-78-7161       TCGA-78-7162       TCGA-78-7163 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-7166       TCGA-78-7167       TCGA-78-7220       TCGA-78-7535 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-7536       TCGA-78-7537       TCGA-78-7539       TCGA-78-7540 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-7542       TCGA-78-7633       TCGA-78-8640       TCGA-78-8648 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-8655       TCGA-78-8660       TCGA-78-8662       TCGA-80-5607 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-80-5608       TCGA-80-5611       TCGA-83-5908       TCGA-86-6562 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-7953       TCGA-86-7954       TCGA-86-7955       TCGA-86-8054 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8073       TCGA-86-8074 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8075       TCGA-86-8076       TCGA-86-8278       TCGA-86-8279 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8280       TCGA-86-8358       TCGA-86-8359       TCGA-86-8585 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-8672 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8673       TCGA-86-8674       TCGA-86-A456       TCGA-86-A4JF 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6828       TCGA-91-6829       TCGA-91-6835 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-91-6840       TCGA-91-A4BD       TCGA-93-7347       TCGA-93-7348 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-93-A4JP 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-93-A4JQ       TCGA-95-7562       TCGA-95-7944       TCGA-95-7947 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-95-7948       TCGA-95-8039       TCGA-95-A4VK       TCGA-95-A4VN 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-97-7546       TCGA-97-7554       TCGA-97-7938       TCGA-97-7941 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-97-8176       TCGA-97-A4M2       TCGA-97-A4M7       TCGA-99-7458 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-99-8025       TCGA-99-8028       TCGA-99-8032       TCGA-99-8033 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-J2-A4AD       TCGA-J2-A4AE       TCGA-J2-A4AG       TCGA-L4-A4E5 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-L4-A4E6       TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5       TCGA-MP-A4SV       TCGA-MP-A4SW 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MP-A4SY       TCGA-MP-A4T2       TCGA-MP-A4T6       TCGA-MP-A4T7 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MP-A4T8       TCGA-MP-A4T9       TCGA-MP-A4TA       TCGA-MP-A4TC 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MP-A4TD       TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MP-A4TI       TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YQ 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM49 MUTATED                                  0     0
  TMEM49 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TMEM49 MUTATED                           0     5
  TMEM49 WILD-TYPE                        29   372
D56V14, multiclass
                                  clus
vv                                 TMEM49 MUTATED TMEM49 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               29
  WHITE                                         5              372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, binary
                  cls
clus                 0   1
  TMEM49 MUTATED     0   4
  TMEM49 WILD-TYPE   6 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM49 MUTATED      0    4
  TMEM49 WILD-TYPE    6  345
                        clus
vv                       TMEM49 MUTATED TMEM49 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4              345
[1] 2 2
[1] FALSE

Clustering(57) Variable = HSPA8 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2               0   1
  HSPA8 MUTATED     5   4
  HSPA8 WILD-TYPE 297 151
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              9             448 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              4             151 
$`HSPA8 MUTATED`
TCGA-50-5946 TCGA-53-7624 TCGA-55-1592 TCGA-69-7978 TCGA-73-4666 TCGA-78-7147 
       22.55        34.29        23.05         4.41        26.30        19.27 
TCGA-78-7542 TCGA-86-8056 TCGA-86-8358 
       10.55         4.57        21.47 

$`HSPA8 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.33        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 
       15.12         9.37        29.03        25.12        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        36.99         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       35.21        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 
        2.01         6.90        52.60        23.38        82.68        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16         5.69        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.20        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  HSPA8 MUTATED HSPA8 WILD-TYPE 
           4.41            0.00 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
          34.29          238.29 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
          21.47           19.79 
[1] "4.4 - 34.3 (21.5)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "2"  
D57V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HSPA8 MUTATED         0        2        2         0         2          1
  HSPA8 WILD-TYPE       4      121      130        47        64         69
                 vv
clus              STAGE IIIB STAGE IV
  HSPA8 MUTATED            0        2
  HSPA8 WILD-TYPE         11       23
D57V3, multiclass
            clus
vv           HSPA8 MUTATED HSPA8 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               2             130
  STAGE IIA              0              47
  STAGE IIB              2              64
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HSPA8 MUTATED     2   6   0   1
  HSPA8 WILD-TYPE 153 255  43  17
D57V4, multiclass
    clus
vv   HSPA8 MUTATED HSPA8 WILD-TYPE
  T1             2             153
  T2             6             255
  T3             0              43
  T4             1              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
  HSPA8 MUTATED     7   2     0
  HSPA8 WILD-TYPE 300  87    72
D57V5, multiclass
       clus
vv      HSPA8 MUTATED HSPA8 WILD-TYPE
  N0                7             300
  N1                2              87
  N2+N3             0              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                 cls
clus                0   1
  HSPA8 MUTATED     5   2
  HSPA8 WILD-TYPE 323  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      5    2
  HSPA8 WILD-TYPE  323   21
   clus
vv  HSPA8 MUTATED HSPA8 WILD-TYPE
  0             5             323
  1             2              21
[1] 2 2
[1] FALSE
D57V7, binary
                 cls
clus                0   1
  HSPA8 MUTATED     4   5
  HSPA8 WILD-TYPE 255 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      4    5
  HSPA8 WILD-TYPE  255  216
        clus
vv       HSPA8 MUTATED HSPA8 WILD-TYPE
  FEMALE             4             255
  MALE               5             216
[1] 2 2
[1] FALSE
D57V8, binary
                 cls
clus                0   1
  HSPA8 MUTATED     6   1
  HSPA8 WILD-TYPE 327  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      6    1
  HSPA8 WILD-TYPE  327   48
     clus
vv    HSPA8 MUTATED HSPA8 WILD-TYPE
  NO              6             327
  YES             1              48
[1] 2 2
[1] FALSE
D57V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HSPA8 MUTATED                            0                                 3
  HSPA8 WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HSPA8 MUTATED                                                    6
  HSPA8 WILD-TYPE                                                289
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HSPA8 MUTATED                                            0
  HSPA8 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HSPA8 MUTATED                                               0
  HSPA8 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  HSPA8 MUTATED                                0
  HSPA8 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  HSPA8 MUTATED                                    0
  HSPA8 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HSPA8 MUTATED                              0                             0
  HSPA8 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HSPA8 MUTATED                                               0
  HSPA8 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  HSPA8 MUTATED                              0
  HSPA8 WILD-TYPE                            9
D57V10, multiclass
                                                    clus
vv                                                   HSPA8 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   HSPA8 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
D57V12, continuous
                 vv
clus               R0  R1  R2  RX
  HSPA8 MUTATED     7   0   0   0
  HSPA8 WILD-TYPE 303  11   4  25
D57V13, multiclass
    clus
vv   HSPA8 MUTATED HSPA8 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSPA8 MUTATED                                  0     0
  HSPA8 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HSPA8 MUTATED                           0     9
  HSPA8 WILD-TYPE                        29   368
D57V14, multiclass
                                  clus
vv                                 HSPA8 MUTATED HSPA8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V15, binary
                 cls
clus                0   1
  HSPA8 MUTATED     1   5
  HSPA8 WILD-TYPE   5 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      1    5
  HSPA8 WILD-TYPE    5  344
                        clus
vv                       HSPA8 MUTATED HSPA8 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(58) Variable = CD244 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  CD244 MUTATED     7   4
  CD244 WILD-TYPE 295 151
  CD244 MUTATED CD244 WILD-TYPE 
             11             446 
  CD244 MUTATED CD244 WILD-TYPE 
              4             151 
$`CD244 MUTATED`
TCGA-44-2656 TCGA-44-7670 TCGA-44-7672 TCGA-50-5045 TCGA-55-8092 TCGA-55-8096 
       46.98        29.00        13.74        71.47         5.06        23.64 
TCGA-55-8506 TCGA-69-7979 TCGA-78-7220 TCGA-86-8358 TCGA-97-A4M5 
        0.36         2.93        26.53        21.47        20.84 

$`CD244 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
       44.61        14.73        26.30         4.37        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       36.07        18.87        29.23        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        20.52        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        0.13        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         4.41        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24        17.16         2.01         6.90        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        50.33       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 
        9.57       104.19       238.29         8.48        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        19.76        20.52        17.75        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        6.35        10.09        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  CD244 MUTATED CD244 WILD-TYPE 
           0.36            0.00 
  CD244 MUTATED CD244 WILD-TYPE 
          71.47          238.29 
  CD244 MUTATED CD244 WILD-TYPE 
         21.470          19.745 
[1] "0.4 - 71.5 (21.5)"  "0.0 - 238.3 (19.7)"
[1] "hr=" "1.1"
D58V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CD244 MUTATED         0        3        5         1         2          1
  CD244 WILD-TYPE       4      120      127        46        64         69
                 vv
clus              STAGE IIIB STAGE IV
  CD244 MUTATED            0        0
  CD244 WILD-TYPE         11       25
D58V3, multiclass
            clus
vv           CD244 MUTATED CD244 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               5             127
  STAGE IIA              1              46
  STAGE IIB              2              64
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CD244 MUTATED     3   7   2   0
  CD244 WILD-TYPE 152 254  41  18
D58V4, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  T1             3             152
  T2             7             254
  T3             2              41
  T4             0              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
  CD244 MUTATED     9   2     1
  CD244 WILD-TYPE 298  87    71
D58V5, multiclass
       clus
vv      CD244 MUTATED CD244 WILD-TYPE
  N0                9             298
  N1                2              87
  N2+N3             1              71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                 cls
clus                0   1
  CD244 MUTATED     8   0
  CD244 WILD-TYPE 320  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      8    0
  CD244 WILD-TYPE  320   23
   clus
vv  CD244 MUTATED CD244 WILD-TYPE
  0             8             320
  1             0              23
[1] 2 2
[1] FALSE
D58V7, binary
                 cls
clus                0   1
  CD244 MUTATED     8   4
  CD244 WILD-TYPE 251 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      8    4
  CD244 WILD-TYPE  251  217
        clus
vv       CD244 MUTATED CD244 WILD-TYPE
  FEMALE             8             251
  MALE               4             217
[1] 2 2
[1] FALSE
D58V8, binary
                 cls
clus                0   1
  CD244 MUTATED     8   2
  CD244 WILD-TYPE 325  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      8    2
  CD244 WILD-TYPE  325   47
     clus
vv    CD244 MUTATED CD244 WILD-TYPE
  NO              8             325
  YES             2              47
[1] 2 2
[1] FALSE
D58V9, continuous
[1] "Remove cluster labels:" "CD244 MUTATED"         
clus
  CD244 MUTATED CD244 WILD-TYPE 
              2             115 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-44-3396 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-6144      TCGA-44-6147 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-44-A47F      TCGA-49-4486 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-49-4494      TCGA-49-4505      TCGA-49-4506      TCGA-49-4510 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-49-6742      TCGA-49-6743      TCGA-49-6744      TCGA-53-7624 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-7283      TCGA-55-7573      TCGA-55-7725 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7914      TCGA-55-8089      TCGA-55-8205 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-8208      TCGA-55-8507      TCGA-55-8508      TCGA-55-8511 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8619      TCGA-55-8620      TCGA-55-8621 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491      TCGA-55-A492 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8394      TCGA-62-8395      TCGA-62-8397 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-8398      TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-A472      TCGA-64-1677      TCGA-64-1681      TCGA-64-5775 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      TCGA-73-4662      TCGA-73-4666 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4676      TCGA-73-4677 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-73-7498      TCGA-73-7499      TCGA-75-5122      TCGA-83-5908 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-6562      TCGA-86-6851      TCGA-86-7701      TCGA-86-7711 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7953      TCGA-86-7954 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-7955      TCGA-86-8054      TCGA-86-8055      TCGA-86-8056 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-8073      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8280      TCGA-86-8281 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-91-6849      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567      TCGA-99-7458 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CD244 MUTATED                            1                                 2
  CD244 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CD244 MUTATED                                                    9
  CD244 WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CD244 MUTATED                                            0
  CD244 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CD244 MUTATED                                               0
  CD244 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CD244 MUTATED                                0
  CD244 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CD244 MUTATED                                    0
  CD244 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CD244 MUTATED                              0                             0
  CD244 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CD244 MUTATED                                               0
  CD244 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CD244 MUTATED                              0
  CD244 WILD-TYPE                            9
D58V10, multiclass
                                                    clus
vv                                                   CD244 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   CD244 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
D58V12, continuous
                 vv
clus               R0  R1  R2  RX
  CD244 MUTATED     5   0   0   0
  CD244 WILD-TYPE 305  11   4  25
D58V13, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  R0             5             305
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD244 MUTATED                                  0     0
  CD244 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CD244 MUTATED                           1    10
  CD244 WILD-TYPE                        28   367
D58V14, multiclass
                                  clus
vv                                 CD244 MUTATED CD244 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       10             367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, binary
                 cls
clus                0   1
  CD244 MUTATED     1   9
  CD244 WILD-TYPE   5 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      1    9
  CD244 WILD-TYPE    5  340
                        clus
vv                       CD244 MUTATED CD244 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(59) Variable = KIF18B MUTATION ANALYSIS
D59V1, survival
                  sevent
clus2                0   1
  KIF18B MUTATED     3   1
  KIF18B WILD-TYPE 299 154
  KIF18B MUTATED KIF18B WILD-TYPE 
               4              453 
  KIF18B MUTATED KIF18B WILD-TYPE 
               1              154 
$`KIF18B MUTATED`
TCGA-05-4250 TCGA-05-4424 TCGA-64-1676 TCGA-67-3771 
        3.98        30.02        56.81        20.05 

$`KIF18B WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       50.33       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  KIF18B MUTATED KIF18B WILD-TYPE 
            3.98             0.00 
  KIF18B MUTATED KIF18B WILD-TYPE 
           56.81           238.29 
  KIF18B MUTATED KIF18B WILD-TYPE 
          25.035           19.760 
[1] "4.0 - 56.8 (25.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.6"
D59V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KIF18B MUTATED         0        2        0         0         1          1
  KIF18B WILD-TYPE       4      121      132        47        65         69
                  vv
clus               STAGE IIIB STAGE IV
  KIF18B MUTATED            0        0
  KIF18B WILD-TYPE         11       25
D59V3, multiclass
            clus
vv           KIF18B MUTATED KIF18B WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              121
  STAGE IB                0              132
  STAGE IIA               0               47
  STAGE IIB               1               65
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF18B MUTATED     2   0   2   0
  KIF18B WILD-TYPE 153 261  41  18
D59V4, multiclass
    clus
vv   KIF18B MUTATED KIF18B WILD-TYPE
  T1              2              153
  T2              0              261
  T3              2               41
  T4              0               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
  KIF18B MUTATED     3   1     0
  KIF18B WILD-TYPE 304  88    72
D59V5, multiclass
       clus
vv      KIF18B MUTATED KIF18B WILD-TYPE
  N0                 3              304
  N1                 1               88
  N2+N3              0               72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                  cls
clus                 0   1
  KIF18B MUTATED     4   0
  KIF18B WILD-TYPE 324  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      4    0
  KIF18B WILD-TYPE  324   23
   clus
vv  KIF18B MUTATED KIF18B WILD-TYPE
  0              4              324
  1              0               23
[1] 2 2
[1] FALSE
D59V7, binary
                  cls
clus                 0   1
  KIF18B MUTATED     2   2
  KIF18B WILD-TYPE 257 219
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      2    2
  KIF18B WILD-TYPE  257  219
        clus
vv       KIF18B MUTATED KIF18B WILD-TYPE
  FEMALE              2              257
  MALE                2              219
[1] 2 2
[1] FALSE
D59V8, binary
                  cls
clus                 0   1
  KIF18B MUTATED     0   1
  KIF18B WILD-TYPE 333  48
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      0    1
  KIF18B WILD-TYPE  333   48
     clus
vv    KIF18B MUTATED KIF18B WILD-TYPE
  NO               0              333
  YES              1               48
[1] 2 2
[1] FALSE
D59V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KIF18B MUTATED                            0                                 1
  KIF18B WILD-TYPE                         18                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KIF18B MUTATED                                                    3
  KIF18B WILD-TYPE                                                292
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KIF18B MUTATED                                            0
  KIF18B WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KIF18B MUTATED                                               0
  KIF18B WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  KIF18B MUTATED                                0
  KIF18B WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  KIF18B MUTATED                                    0
  KIF18B WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KIF18B MUTATED                              0                             0
  KIF18B WILD-TYPE                            2                            22
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KIF18B MUTATED                                               0
  KIF18B WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  KIF18B MUTATED                              0
  KIF18B WILD-TYPE                            9
D59V10, multiclass
                                                    clus
vv                                                   KIF18B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   KIF18B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
D59V12, continuous
[1] "Remove cluster labels:" "KIF18B MUTATED"        
clus
  KIF18B MUTATED KIF18B WILD-TYPE 
               1              256 
      TCGA-05-4384       TCGA-05-4390       TCGA-05-4396       TCGA-05-4405 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-05-4410       TCGA-05-4415       TCGA-05-4417       TCGA-05-4427 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-05-4433       TCGA-05-5420       TCGA-05-5423       TCGA-05-5425 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-05-5428       TCGA-35-4122       TCGA-35-4123       TCGA-35-5375 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-38-4625       TCGA-38-4626       TCGA-38-7271       TCGA-38-A44F 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-2656       TCGA-44-2657       TCGA-44-3396       TCGA-44-3398 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-3918       TCGA-44-4112       TCGA-44-5644       TCGA-44-5645 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6144       TCGA-44-6145       TCGA-44-6147       TCGA-44-6148 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6774       TCGA-44-6775       TCGA-44-6776       TCGA-44-6777 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6778       TCGA-44-6779       TCGA-44-7659       TCGA-44-7660 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7661       TCGA-44-7662       TCGA-44-7667       TCGA-44-7669 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7670       TCGA-44-7672       TCGA-44-8117       TCGA-44-8119 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-8120       TCGA-44-A479       TCGA-44-A47A       TCGA-44-A47B 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-A47F       TCGA-44-A47G       TCGA-44-A4SS       TCGA-44-A4SU 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4494       TCGA-49-4505       TCGA-53-7624 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-53-7626       TCGA-53-7813       TCGA-53-A4EZ       TCGA-55-1592 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-1595       TCGA-55-5899       TCGA-55-6642       TCGA-55-6712 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6971       TCGA-55-7227       TCGA-55-7283       TCGA-55-7570 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7574       TCGA-55-7576       TCGA-55-7724       TCGA-55-7725 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7726       TCGA-55-7728       TCGA-55-7907       TCGA-55-7910 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7911       TCGA-55-7914       TCGA-55-8089       TCGA-55-8092 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8094       TCGA-55-8096       TCGA-55-8097       TCGA-55-8205 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8299       TCGA-55-8301       TCGA-55-8302       TCGA-55-8506 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8511       TCGA-55-8512       TCGA-55-8514 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8615       TCGA-55-8620       TCGA-55-8621       TCGA-55-A48X 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A492       TCGA-55-A493       TCGA-55-A494       TCGA-62-8398 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-64-1677       TCGA-64-1681       TCGA-64-5774       TCGA-64-5775 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-64-5778       TCGA-64-5779       TCGA-64-5781       TCGA-69-7761 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7763       TCGA-69-7764       TCGA-69-7765       TCGA-69-7974 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7979       TCGA-69-8253       TCGA-69-8255       TCGA-69-A59K 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4662       TCGA-73-4666       TCGA-73-4668 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-4670       TCGA-73-4675       TCGA-73-4676       TCGA-73-7498 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-75-6214       TCGA-75-7025       TCGA-75-7027       TCGA-75-7031 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7145       TCGA-78-7146       TCGA-78-7147       TCGA-78-7148 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7149       TCGA-78-7150       TCGA-78-7152       TCGA-78-7153 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7154       TCGA-78-7155       TCGA-78-7156       TCGA-78-7158 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7159       TCGA-78-7160       TCGA-78-7161       TCGA-78-7162 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7163       TCGA-78-7166       TCGA-78-7167       TCGA-78-7220 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7535       TCGA-78-7536       TCGA-78-7537       TCGA-78-7539 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7542       TCGA-78-7633       TCGA-78-8640       TCGA-78-8648 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-8655       TCGA-78-8660       TCGA-78-8662       TCGA-80-5607 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-80-5608       TCGA-83-5908       TCGA-86-6851       TCGA-86-7711 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7954       TCGA-86-8054       TCGA-86-8055 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8073       TCGA-86-8074       TCGA-86-8281 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8669       TCGA-86-8673 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8674       TCGA-86-A456       TCGA-91-6829       TCGA-91-6830 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-6836       TCGA-91-6840       TCGA-91-6849       TCGA-91-8499 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-A4BC       TCGA-93-7347       TCGA-93-7348       TCGA-93-8067 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-93-A4JQ       TCGA-95-7043 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-7562       TCGA-95-7567       TCGA-95-7944       TCGA-95-7947 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-7948       TCGA-95-A4VK       TCGA-95-A4VN       TCGA-95-A4VP 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-7546       TCGA-97-7553       TCGA-97-7554       TCGA-97-7941 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8171       TCGA-97-8172       TCGA-97-8174       TCGA-97-8176 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8179       TCGA-97-A4LX       TCGA-97-A4M0       TCGA-97-A4M1 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-A4M2       TCGA-97-A4M3       TCGA-97-A4M5       TCGA-97-A4M7 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-99-7458       TCGA-99-8025       TCGA-99-8028       TCGA-99-8032 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-J2-8194       TCGA-J2-A4AD       TCGA-J2-A4AG       TCGA-L4-A4E5 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-L4-A4E6       TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MN-A4N4       TCGA-MN-A4N5       TCGA-MP-A4SV       TCGA-MP-A4SW 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4T2       TCGA-MP-A4T4       TCGA-MP-A4T7       TCGA-MP-A4T8 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4T9       TCGA-MP-A4TA       TCGA-MP-A4TC       TCGA-MP-A4TE 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI       TCGA-MP-A4TK 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A5C7       TCGA-NJ-A4YG       TCGA-NJ-A4YI       TCGA-O1-A52J 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
                  vv
clus                R0  R1  R2  RX
  KIF18B MUTATED     2   1   1   0
  KIF18B WILD-TYPE 308  10   3  25
D59V13, multiclass
    clus
vv   KIF18B MUTATED KIF18B WILD-TYPE
  R0              2              308
  R1              1               10
  R2              1                3
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF18B MUTATED                                  0     0
  KIF18B WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF18B MUTATED                           1     1
  KIF18B WILD-TYPE                        28   376
D59V14, multiclass
[1] "Remove cluster labels:" "KIF18B MUTATED"        
clus
  KIF18B MUTATED KIF18B WILD-TYPE 
               2              412 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-38-4625 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-38-4626       TCGA-38-4627       TCGA-38-4628       TCGA-38-4629 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-38-4630       TCGA-38-4631       TCGA-38-4632       TCGA-38-6178 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-38-7271       TCGA-38-A44F       TCGA-44-2656       TCGA-44-2657 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-2661       TCGA-44-2665       TCGA-44-3396       TCGA-44-3398 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-3918       TCGA-44-3919       TCGA-44-4112       TCGA-44-5643 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-5644       TCGA-44-5645       TCGA-44-6144       TCGA-44-6145 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6146       TCGA-44-6147       TCGA-44-6148       TCGA-44-6774 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6775       TCGA-44-6776       TCGA-44-6777       TCGA-44-6778 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6779       TCGA-44-7659       TCGA-44-7660       TCGA-44-7661 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7662       TCGA-44-7667       TCGA-44-7669       TCGA-44-7670 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7671       TCGA-44-7672       TCGA-44-8117       TCGA-44-8119 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-8120       TCGA-44-A479       TCGA-44-A47A       TCGA-44-A47B 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-A47F       TCGA-44-A47G       TCGA-44-A4SS       TCGA-44-A4SU 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-4486       TCGA-49-4487       TCGA-49-4488       TCGA-49-4490 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-4494       TCGA-49-4501       TCGA-49-4505       TCGA-49-4506 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-4507       TCGA-49-4510       TCGA-49-4512       TCGA-49-4514 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-6742       TCGA-49-6743       TCGA-49-6744       TCGA-49-6745 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-6761       TCGA-49-6767       TCGA-50-5044       TCGA-50-5045 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5049       TCGA-50-5051       TCGA-50-5055       TCGA-50-5066 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5068       TCGA-50-5072       TCGA-50-5930       TCGA-50-5931 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5932       TCGA-50-5933       TCGA-50-5935       TCGA-50-5936 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5939       TCGA-50-5941       TCGA-50-5942       TCGA-50-5944 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5946       TCGA-50-6590       TCGA-50-6591       TCGA-50-6592 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-6593       TCGA-50-6594       TCGA-50-6595       TCGA-50-6597 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-6673       TCGA-50-7109       TCGA-50-8457       TCGA-50-8459 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-8460       TCGA-53-7624       TCGA-53-7626       TCGA-53-7813 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-53-A4EZ       TCGA-55-1592       TCGA-55-1595       TCGA-55-5899 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6543       TCGA-55-6642       TCGA-55-6712       TCGA-55-6968 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6969       TCGA-55-6970       TCGA-55-6971       TCGA-55-6972 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6975       TCGA-55-6978       TCGA-55-6979       TCGA-55-6980 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6981       TCGA-55-6982       TCGA-55-6983       TCGA-55-6984 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6985       TCGA-55-6986       TCGA-55-6987       TCGA-55-7227 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7281       TCGA-55-7283       TCGA-55-7284       TCGA-55-7570 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7573       TCGA-55-7574       TCGA-55-7576       TCGA-55-7724 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7726       TCGA-55-7727       TCGA-55-7816 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7903       TCGA-55-7907       TCGA-55-7910       TCGA-55-7911 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7914       TCGA-55-7994       TCGA-55-7995       TCGA-55-8085 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8087       TCGA-55-8089       TCGA-55-8090       TCGA-55-8091 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8092       TCGA-55-8094       TCGA-55-8096       TCGA-55-8097 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8203       TCGA-55-8204       TCGA-55-8205       TCGA-55-8206 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8207       TCGA-55-8208       TCGA-55-8299       TCGA-55-8301 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8302       TCGA-55-8505       TCGA-55-8506       TCGA-55-8507 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8508       TCGA-55-8510       TCGA-55-8511       TCGA-55-8512 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8513       TCGA-55-8514       TCGA-55-8614       TCGA-55-8615 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8616       TCGA-55-8619       TCGA-55-8620       TCGA-55-8621 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A48X       TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A491       TCGA-55-A492       TCGA-55-A493       TCGA-55-A494 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A4DF       TCGA-55-A4DG       TCGA-62-8394       TCGA-62-8395 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1679 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-64-1681       TCGA-64-5774       TCGA-64-5775       TCGA-64-5778 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-64-5779       TCGA-64-5781       TCGA-64-5815       TCGA-67-3772 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-67-3773       TCGA-67-4679       TCGA-67-6215       TCGA-67-6216 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-67-6217       TCGA-69-7760       TCGA-69-7761       TCGA-69-7763 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7764       TCGA-69-7765       TCGA-69-7973       TCGA-69-7974 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7978       TCGA-69-7979       TCGA-69-7980       TCGA-69-8253 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-8254       TCGA-69-8255       TCGA-69-A59K       TCGA-71-6725 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4658       TCGA-73-4659       TCGA-73-4662 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-4666       TCGA-73-4668       TCGA-73-4670       TCGA-73-4675 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-4676       TCGA-73-4677       TCGA-73-7498       TCGA-73-7499 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7143       TCGA-78-7145       TCGA-78-7146       TCGA-78-7147 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7148       TCGA-78-7149       TCGA-78-7150       TCGA-78-7152 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7153       TCGA-78-7154       TCGA-78-7155       TCGA-78-7156 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7158       TCGA-78-7159       TCGA-78-7160       TCGA-78-7161 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7162       TCGA-78-7163       TCGA-78-7166       TCGA-78-7167 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7220       TCGA-78-7535       TCGA-78-7536       TCGA-78-7539 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7540       TCGA-78-7542       TCGA-78-7633       TCGA-83-5908 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-6562       TCGA-86-6851       TCGA-86-7701       TCGA-86-7711 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7953       TCGA-86-7954 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-7955       TCGA-86-8054       TCGA-86-8055       TCGA-86-8056 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8073       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8280       TCGA-86-8281 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8585       TCGA-86-8668 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8669       TCGA-86-8671       TCGA-86-8672       TCGA-86-8673 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8674       TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-A4P8       TCGA-91-6828       TCGA-91-6829       TCGA-91-6830 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-6831       TCGA-91-6835       TCGA-91-6836       TCGA-91-6840 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-6847       TCGA-91-6848       TCGA-91-6849       TCGA-91-7771 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-8496       TCGA-91-8497       TCGA-91-8499       TCGA-91-A4BC 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-A4BD       TCGA-93-7347       TCGA-93-7348       TCGA-93-8067 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-93-A4JP       TCGA-93-A4JQ 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-7039       TCGA-95-7043       TCGA-95-7562       TCGA-95-7567 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-7944       TCGA-95-7947       TCGA-95-7948       TCGA-95-8039 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-8494       TCGA-95-A4VK       TCGA-95-A4VN       TCGA-95-A4VP 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-7546       TCGA-97-7547       TCGA-97-7552       TCGA-97-7553 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-7554       TCGA-97-7937       TCGA-97-7938       TCGA-97-7941 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8171       TCGA-97-8172       TCGA-97-8174       TCGA-97-8175 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8176       TCGA-97-8177       TCGA-97-8179       TCGA-97-8552 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-A4LX       TCGA-97-A4M0       TCGA-97-A4M1       TCGA-97-A4M2 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-A4M3       TCGA-97-A4M5       TCGA-97-A4M6       TCGA-97-A4M7 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-99-7458       TCGA-99-8025       TCGA-99-8028       TCGA-99-8032 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-99-8033       TCGA-J2-8192       TCGA-J2-8194       TCGA-J2-A4AD 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-J2-A4AE       TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1       TCGA-MN-A4N4 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MN-A4N5       TCGA-MP-A4SW       TCGA-MP-A4SY       TCGA-MP-A4T2 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T9       TCGA-MP-A4TA 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TC       TCGA-MP-A4TD       TCGA-MP-A4TE       TCGA-MP-A4TF 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TH       TCGA-MP-A4TI       TCGA-MP-A5C7       TCGA-NJ-A4YF 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-NJ-A4YG       TCGA-NJ-A4YI       TCGA-NJ-A4YP       TCGA-NJ-A4YQ 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-NJ-A55A       TCGA-NJ-A55O       TCGA-NJ-A55R       TCGA-O1-A52J 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
D59V15, binary
                  cls
clus                 0   1
  KIF18B MUTATED     0   2
  KIF18B WILD-TYPE   6 347
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      0    2
  KIF18B WILD-TYPE    6  347
                        clus
vv                       KIF18B MUTATED KIF18B WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              2              347
[1] 2 2
[1] FALSE

Clustering(60) Variable = PDE6A MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2               0   1
  PDE6A MUTATED    11   5
  PDE6A WILD-TYPE 291 150
  PDE6A MUTATED PDE6A WILD-TYPE 
             16             441 
  PDE6A MUTATED PDE6A WILD-TYPE 
              5             150 
$`PDE6A MUTATED`
TCGA-05-4382 TCGA-44-5644 TCGA-53-7624 TCGA-55-6642 TCGA-55-6972 TCGA-55-8299 
       19.96        28.37        34.29        32.65        48.49        15.42 
TCGA-55-8507 TCGA-55-A4DG TCGA-62-A46O TCGA-67-3771 TCGA-73-4659 TCGA-73-4668 
        0.26        19.99        47.80        20.05        23.38        15.35 
TCGA-91-6828 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-NJ-A4YQ 
       10.62        27.19        31.23        29.13 

$`PDE6A WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.99         7.59        27.25        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       23.05        48.62         2.86         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16         1.45         0.76         0.95         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        20.19         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        88.64        49.25        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
        2.01         6.90        52.60        82.68        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       26.50        29.46        24.23        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC 
       86.04        58.85         5.49         5.29        41.59         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       73.91        71.05        62.60         0.13         1.64         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  PDE6A MUTATED PDE6A WILD-TYPE 
           0.26            0.00 
  PDE6A MUTATED PDE6A WILD-TYPE 
          48.49          238.29 
  PDE6A MUTATED PDE6A WILD-TYPE 
         25.285          19.590 
[1] "0.3 - 48.5 (25.3)"  "0.0 - 238.3 (19.6)"
[1] "hr=" "1.1"
D60V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PDE6A MUTATED         0        7        5         1         1          1
  PDE6A WILD-TYPE       4      116      127        46        65         69
                 vv
clus              STAGE IIIB STAGE IV
  PDE6A MUTATED            0        1
  PDE6A WILD-TYPE         11       24
D60V3, multiclass
            clus
vv           PDE6A MUTATED PDE6A WILD-TYPE
  STAGE I                0               4
  STAGE IA               7             116
  STAGE IB               5             127
  STAGE IIA              1              46
  STAGE IIB              1              65
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDE6A MUTATED     7   9   0   0
  PDE6A WILD-TYPE 148 252  43  18
D60V4, multiclass
    clus
vv   PDE6A MUTATED PDE6A WILD-TYPE
  T1             7             148
  T2             9             252
  T3             0              43
  T4             0              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
  PDE6A MUTATED    13   2     1
  PDE6A WILD-TYPE 294  87    71
D60V5, multiclass
       clus
vv      PDE6A MUTATED PDE6A WILD-TYPE
  N0               13             294
  N1                2              87
  N2+N3             1              71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                 cls
clus                0   1
  PDE6A MUTATED    10   1
  PDE6A WILD-TYPE 318  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED     10    1
  PDE6A WILD-TYPE  318   22
   clus
vv  PDE6A MUTATED PDE6A WILD-TYPE
  0            10             318
  1             1              22
[1] 2 2
[1] FALSE
D60V7, binary
                 cls
clus                0   1
  PDE6A MUTATED     8   8
  PDE6A WILD-TYPE 251 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED      8    8
  PDE6A WILD-TYPE  251  213
        clus
vv       PDE6A MUTATED PDE6A WILD-TYPE
  FEMALE             8             251
  MALE               8             213
[1] 2 2
[1] FALSE
D60V8, binary
                 cls
clus                0   1
  PDE6A MUTATED    11   0
  PDE6A WILD-TYPE 322  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED     11    0
  PDE6A WILD-TYPE  322   49
     clus
vv    PDE6A MUTATED PDE6A WILD-TYPE
  NO             11             322
  YES             0              49
[1] 2 2
[1] FALSE
D60V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PDE6A MUTATED                            0                                 1
  PDE6A WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PDE6A MUTATED                                                   13
  PDE6A WILD-TYPE                                                282
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PDE6A MUTATED                                            0
  PDE6A WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PDE6A MUTATED                                               0
  PDE6A WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  PDE6A MUTATED                                0
  PDE6A WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  PDE6A MUTATED                                    1
  PDE6A WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PDE6A MUTATED                              0                             1
  PDE6A WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PDE6A MUTATED                                               0
  PDE6A WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  PDE6A MUTATED                              0
  PDE6A WILD-TYPE                            9
D60V10, multiclass
                                                    clus
vv                                                   PDE6A MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   PDE6A WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
D60V12, continuous
                 vv
clus               R0  R1  R2  RX
  PDE6A MUTATED    14   0   0   1
  PDE6A WILD-TYPE 296  11   4  24
D60V13, multiclass
    clus
vv   PDE6A MUTATED PDE6A WILD-TYPE
  R0            14             296
  R1             0              11
  R2             0               4
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDE6A MUTATED                                  1     0
  PDE6A WILD-TYPE                                0     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDE6A MUTATED                           2    12
  PDE6A WILD-TYPE                        27   365
D60V14, multiclass
                                  clus
vv                                 PDE6A MUTATED PDE6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              27
  WHITE                                       12             365
[1] 4 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
  PDE6A MUTATED     1  13
  PDE6A WILD-TYPE   5 336
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED      1   13
  PDE6A WILD-TYPE    5  336
                        clus
vv                       PDE6A MUTATED PDE6A WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            13             336
[1] 2 2
[1] FALSE

Clustering(61) Variable = CHRND MUTATION ANALYSIS
D61V1, survival
                 sevent
clus2               0   1
  CHRND MUTATED    13   2
  CHRND WILD-TYPE 289 153
  CHRND MUTATED CHRND WILD-TYPE 
             15             442 
  CHRND MUTATED CHRND WILD-TYPE 
              2             153 
$`CHRND MUTATED`
TCGA-05-4418 TCGA-05-4420 TCGA-05-4432 TCGA-38-4632 TCGA-44-3918 TCGA-44-5644 
        9.01        29.98        25.02        44.61        34.06        28.37 
TCGA-44-7662 TCGA-50-5049 TCGA-50-8459 TCGA-55-7907 TCGA-55-A492 TCGA-62-8399 
        7.17        70.55         7.59         0.53        19.59        88.64 
TCGA-64-5778 TCGA-86-8358 TCGA-95-7947 
       42.90        21.47        15.68 

$`CHRND WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       20.05         2.99        14.96        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        26.01        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        11.64        14.73        26.30         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       46.98        44.42        38.10        42.77        37.15        38.24 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       33.73        26.56        33.30        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
       17.16        11.64        22.26        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.99        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.45        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1.58        20.58         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        42.38        14.60        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98         2.04        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.04        31.20        23.05        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29        41.82        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  CHRND MUTATED CHRND WILD-TYPE 
           0.53            0.00 
  CHRND MUTATED CHRND WILD-TYPE 
          88.64          238.29 
  CHRND MUTATED CHRND WILD-TYPE 
         25.020          19.745 
[1] "0.5 - 88.6 (25.0)"  "0.0 - 238.3 (19.7)"
[1] "hr=" "3.2"
D61V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CHRND MUTATED         0        4        6         1         2          2
  CHRND WILD-TYPE       4      119      126        46        64         68
                 vv
clus              STAGE IIIB STAGE IV
  CHRND MUTATED            0        1
  CHRND WILD-TYPE         11       24
D61V3, multiclass
            clus
vv           CHRND MUTATED CHRND WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               6             126
  STAGE IIA              1              46
  STAGE IIB              2              64
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHRND MUTATED     3  11   2   0
  CHRND WILD-TYPE 152 250  41  18
D61V4, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  T1             3             152
  T2            11             250
  T3             2              41
  T4             0              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
  CHRND MUTATED    11   3     2
  CHRND WILD-TYPE 296  86    70
D61V5, multiclass
       clus
vv      CHRND MUTATED CHRND WILD-TYPE
  N0               11             296
  N1                3              86
  N2+N3             2              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                 cls
clus                0   1
  CHRND MUTATED    11   1
  CHRND WILD-TYPE 317  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED     11    1
  CHRND WILD-TYPE  317   22
   clus
vv  CHRND MUTATED CHRND WILD-TYPE
  0            11             317
  1             1              22
[1] 2 2
[1] FALSE
D61V7, binary
                 cls
clus                0   1
  CHRND MUTATED     4  12
  CHRND WILD-TYPE 255 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      4   12
  CHRND WILD-TYPE  255  209
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  FEMALE             4             255
  MALE              12             209
[1] 2 2
[1] FALSE
D61V8, binary
                 cls
clus                0   1
  CHRND MUTATED    13   1
  CHRND WILD-TYPE 320  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED     13    1
  CHRND WILD-TYPE  320   48
     clus
vv    CHRND MUTATED CHRND WILD-TYPE
  NO             13             320
  YES             1              48
[1] 2 2
[1] FALSE
D61V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CHRND MUTATED                            0                                 4
  CHRND WILD-TYPE                         18                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CHRND MUTATED                                                    9
  CHRND WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  CHRND MUTATED                                            0
  CHRND WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  CHRND MUTATED                                               1
  CHRND WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  CHRND MUTATED                                0
  CHRND WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  CHRND MUTATED                                    0
  CHRND WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  CHRND MUTATED                              0                             1
  CHRND WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  CHRND MUTATED                                               0
  CHRND WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  CHRND MUTATED                              1
  CHRND WILD-TYPE                            8
D61V10, multiclass
                                                    clus
vv                                                   CHRND MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   1
                                                    clus
vv                                                   CHRND WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, continuous
D61V12, continuous
                 vv
clus               R0  R1  R2  RX
  CHRND MUTATED    12   0   0   0
  CHRND WILD-TYPE 298  11   4  25
D61V13, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  R0            12             298
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRND MUTATED                                  0     0
  CHRND WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHRND MUTATED                           1    11
  CHRND WILD-TYPE                        28   366
D61V14, multiclass
                                  clus
vv                                 CHRND MUTATED CHRND WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       11             366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V15, binary
                 cls
clus                0   1
  CHRND MUTATED     0  12
  CHRND WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      0   12
  CHRND WILD-TYPE    6  337
                        clus
vv                       CHRND MUTATED CHRND WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(62) Variable = KLK1 MUTATION ANALYSIS
D62V1, survival
                sevent
clus2              0   1
  KLK1 MUTATED     6   2
  KLK1 WILD-TYPE 296 153
  KLK1 MUTATED KLK1 WILD-TYPE 
             8            449 
  KLK1 MUTATED KLK1 WILD-TYPE 
             2            153 
$`KLK1 MUTATED`
TCGA-05-4390 TCGA-50-5935 TCGA-53-A4EZ TCGA-55-6968 TCGA-62-8399 TCGA-69-7765 
       37.02        21.47        35.21        42.51        88.64         5.42 
TCGA-69-7978 TCGA-86-8673 
        4.41        28.34 

$`KLK1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        78.67         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
       19.99         4.57        39.98        42.38        14.60        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       51.25        28.47        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
       13.61         7.56         6.05         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58         0.62        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29        41.82        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  KLK1 MUTATED KLK1 WILD-TYPE 
          4.41           0.00 
  KLK1 MUTATED KLK1 WILD-TYPE 
         88.64         238.29 
  KLK1 MUTATED KLK1 WILD-TYPE 
        31.775         19.730 
[1] "4.4 - 88.6 (31.8)"  "0.0 - 238.3 (19.7)"
[1] "hr=" "1.9"
D62V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KLK1 MUTATED         0        1        2         1         1          1
  KLK1 WILD-TYPE       4      122      130        46        65         69
                vv
clus             STAGE IIIB STAGE IV
  KLK1 MUTATED            0        2
  KLK1 WILD-TYPE         11       23
D62V3, multiclass
            clus
vv           KLK1 MUTATED KLK1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              2            130
  STAGE IIA             1             46
  STAGE IIB             1             65
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              2             23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLK1 MUTATED     2   5   0   1
  KLK1 WILD-TYPE 153 256  43  17
D62V4, multiclass
    clus
vv   KLK1 MUTATED KLK1 WILD-TYPE
  T1            2            153
  T2            5            256
  T3            0             43
  T4            1             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
  KLK1 MUTATED     5   2     1
  KLK1 WILD-TYPE 302  87    71
D62V5, multiclass
       clus
vv      KLK1 MUTATED KLK1 WILD-TYPE
  N0               5            302
  N1               2             87
  N2+N3            1             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                cls
clus               0   1
  KLK1 MUTATED     4   1
  KLK1 WILD-TYPE 324  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK1 MUTATED      4    1
  KLK1 WILD-TYPE  324   22
   clus
vv  KLK1 MUTATED KLK1 WILD-TYPE
  0            4            324
  1            1             22
[1] 2 2
[1] FALSE
D62V7, binary
                cls
clus               0   1
  KLK1 MUTATED     2   6
  KLK1 WILD-TYPE 257 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK1 MUTATED      2    6
  KLK1 WILD-TYPE  257  215
        clus
vv       KLK1 MUTATED KLK1 WILD-TYPE
  FEMALE            2            257
  MALE              6            215
[1] 2 2
[1] FALSE
D62V8, binary
                cls
clus               0   1
  KLK1 MUTATED     5   3
  KLK1 WILD-TYPE 328  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK1 MUTATED      5    3
  KLK1 WILD-TYPE  328   46
     clus
vv    KLK1 MUTATED KLK1 WILD-TYPE
  NO             5            328
  YES            3             46
[1] 2 2
[1] FALSE
D62V9, continuous
[1] "Remove cluster labels:" "KLK1 MUTATED"          
clus
  KLK1 MUTATED KLK1 WILD-TYPE 
             2            115 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-44-3396 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-6144     TCGA-44-6147 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-44-A47F     TCGA-49-4486 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-49-4494     TCGA-49-4505     TCGA-49-4506     TCGA-49-4510 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-49-6742     TCGA-49-6743     TCGA-49-6744     TCGA-53-7624 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-8621 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-64-1677     TCGA-64-1681     TCGA-64-5775     TCGA-64-5778 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8254     TCGA-71-6725     TCGA-71-8520 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-73-4659     TCGA-73-4662     TCGA-73-4666     TCGA-73-4668 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4676     TCGA-73-4677     TCGA-73-7498 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-73-7499     TCGA-75-5122     TCGA-83-5908     TCGA-86-6562 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-6851     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7953     TCGA-86-7954     TCGA-86-7955 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8280     TCGA-86-8281     TCGA-86-8358 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6829 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-91-6849     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-95-7567     TCGA-99-7458 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KLK1 MUTATED                            1                                 3
  KLK1 WILD-TYPE                         17                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KLK1 MUTATED                                                    2
  KLK1 WILD-TYPE                                                293
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KLK1 MUTATED                                            0
  KLK1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KLK1 MUTATED                                               1
  KLK1 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  KLK1 MUTATED                                0
  KLK1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  KLK1 MUTATED                                    0
  KLK1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KLK1 MUTATED                              0                             1
  KLK1 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KLK1 MUTATED                                               0
  KLK1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  KLK1 MUTATED                              0
  KLK1 WILD-TYPE                            9
D62V10, multiclass
                                                    clus
vv                                                   KLK1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   KLK1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
D62V12, continuous
                vv
clus              R0  R1  R2  RX
  KLK1 MUTATED     3   0   0   1
  KLK1 WILD-TYPE 307  11   4  24
D62V13, multiclass
    clus
vv   KLK1 MUTATED KLK1 WILD-TYPE
  R0            3            307
  R1            0             11
  R2            0              4
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLK1 MUTATED                                  0     0
  KLK1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KLK1 MUTATED                           1     6
  KLK1 WILD-TYPE                        28   371
D62V14, multiclass
                                  clus
vv                                 KLK1 MUTATED KLK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       6            371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V15, binary
                cls
clus               0   1
  KLK1 MUTATED     1   6
  KLK1 WILD-TYPE   5 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK1 MUTATED      1    6
  KLK1 WILD-TYPE    5  343
                        clus
vv                       KLK1 MUTATED KLK1 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO            6            343
[1] 2 2
[1] FALSE

Clustering(63) Variable = KLHL5 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2               0   1
  KLHL5 MUTATED    11   3
  KLHL5 WILD-TYPE 291 152
  KLHL5 MUTATED KLHL5 WILD-TYPE 
             14             443 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
              3             152 
$`KLHL5 MUTATED`
TCGA-44-2657 TCGA-44-3918 TCGA-44-7661 TCGA-44-8120 TCGA-44-A4SS TCGA-49-4486 
       44.42        34.06        12.03         8.55        13.64        76.21 
TCGA-55-7284 TCGA-55-A4DG TCGA-69-8255 TCGA-86-7711 TCGA-91-6836 TCGA-95-7947 
        7.99        19.99         4.24        34.39        13.71        15.68 
TCGA-95-A4VN TCGA-NJ-A4YQ 
       18.18        29.13 

$`KLHL5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 
       44.61        14.73        26.30         4.37        46.98        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        38.24        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 
       29.00        29.23        13.74        12.66         3.25        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4487 
       15.32         9.44        11.08        11.54        13.45        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        8.81        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.33        17.16        11.64        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       30.54        13.94        35.21        23.05        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 
       70.26         1.74         0.59         1.15         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        20.19         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41         2.93        12.56        14.01        13.45 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        31.13        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 
       16.54         2.86        18.67        12.39        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
        2.76        21.40        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64         0.26         0.43        19.82        59.11 

  KLHL5 MUTATED KLHL5 WILD-TYPE 
           4.24            0.00 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
          76.21          238.29 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
          16.93           19.82 
[1] "4.2 - 76.2 (16.9)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.5"
D63V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KLHL5 MUTATED         0        7        4         2         1          0
  KLHL5 WILD-TYPE       4      116      128        45        65         70
                 vv
clus              STAGE IIIB STAGE IV
  KLHL5 MUTATED            0        0
  KLHL5 WILD-TYPE         11       25
D63V3, multiclass
            clus
vv           KLHL5 MUTATED KLHL5 WILD-TYPE
  STAGE I                0               4
  STAGE IA               7             116
  STAGE IB               4             128
  STAGE IIA              2              45
  STAGE IIB              1              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLHL5 MUTATED     7   6   1   0
  KLHL5 WILD-TYPE 148 255  42  18
D63V4, multiclass
    clus
vv   KLHL5 MUTATED KLHL5 WILD-TYPE
  T1             7             148
  T2             6             255
  T3             1              42
  T4             0              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
  KLHL5 MUTATED    11   2     0
  KLHL5 WILD-TYPE 296  87    72
D63V5, multiclass
       clus
vv      KLHL5 MUTATED KLHL5 WILD-TYPE
  N0               11             296
  N1                2              87
  N2+N3             0              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                 cls
clus                0   1
  KLHL5 MUTATED    11   0
  KLHL5 WILD-TYPE 317  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED     11    0
  KLHL5 WILD-TYPE  317   23
   clus
vv  KLHL5 MUTATED KLHL5 WILD-TYPE
  0            11             317
  1             0              23
[1] 2 2
[1] FALSE
D63V7, binary
                 cls
clus                0   1
  KLHL5 MUTATED     6   8
  KLHL5 WILD-TYPE 253 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED      6    8
  KLHL5 WILD-TYPE  253  213
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  FEMALE             6             253
  MALE               8             213
[1] 2 2
[1] FALSE
D63V8, binary
                 cls
clus                0   1
  KLHL5 MUTATED    14   0
  KLHL5 WILD-TYPE 319  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED     14    0
  KLHL5 WILD-TYPE  319   49
     clus
vv    KLHL5 MUTATED KLHL5 WILD-TYPE
  NO             14             319
  YES             0              49
[1] 2 2
[1] FALSE
D63V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KLHL5 MUTATED                            0                                 1
  KLHL5 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KLHL5 MUTATED                                                   10
  KLHL5 WILD-TYPE                                                285
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  KLHL5 MUTATED                                            0
  KLHL5 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  KLHL5 MUTATED                                               1
  KLHL5 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  KLHL5 MUTATED                                0
  KLHL5 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  KLHL5 MUTATED                                    0
  KLHL5 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  KLHL5 MUTATED                              0                             0
  KLHL5 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  KLHL5 MUTATED                                               2
  KLHL5 WILD-TYPE                                             3
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  KLHL5 MUTATED                              0
  KLHL5 WILD-TYPE                            9
D63V10, multiclass
                                                    clus
vv                                                   KLHL5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            10
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  2
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   KLHL5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
D63V12, continuous
                 vv
clus               R0  R1  R2  RX
  KLHL5 MUTATED     8   0   0   1
  KLHL5 WILD-TYPE 302  11   4  24
D63V13, multiclass
    clus
vv   KLHL5 MUTATED KLHL5 WILD-TYPE
  R0             8             302
  R1             0              11
  R2             0               4
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLHL5 MUTATED                                  0     0
  KLHL5 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLHL5 MUTATED                           1    13
  KLHL5 WILD-TYPE                        28   364
D63V14, multiclass
                                  clus
vv                                 KLHL5 MUTATED KLHL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       13             364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V15, binary
                 cls
clus                0   1
  KLHL5 MUTATED     2  12
  KLHL5 WILD-TYPE   4 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED      2   12
  KLHL5 WILD-TYPE    4  337
                        clus
vv                       KLHL5 MUTATED KLHL5 WILD-TYPE
  HISPANIC OR LATINO                 2               4
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(64) Variable = DSC2 MUTATION ANALYSIS
D64V1, survival
                sevent
clus2              0   1
  DSC2 MUTATED    14   6
  DSC2 WILD-TYPE 288 149
  DSC2 MUTATED DSC2 WILD-TYPE 
            20            437 
  DSC2 MUTATED DSC2 WILD-TYPE 
             6            149 
$`DSC2 MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-44-2657 TCGA-44-7662 TCGA-44-7670 TCGA-49-6742 
       19.96        14.01        44.42         7.17        29.00        16.04 
TCGA-49-6743 TCGA-53-7626 TCGA-55-7576 TCGA-55-8207 TCGA-55-8507 TCGA-55-8508 
       53.29        30.54         1.32         2.17         0.26         0.49 
TCGA-69-A59K TCGA-78-7542 TCGA-86-8073 TCGA-97-7554 TCGA-97-7938 TCGA-MP-A4TC 
       17.16        10.55        24.33        25.48         0.59         2.43 
TCGA-NJ-A4YI TCGA-NJ-A4YP 
        0.13         1.64 

$`DSC2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        45.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        46.98        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       22.72        19.46        12.03        36.07        18.87        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 
       32.84         8.81        29.46        29.75        55.89        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
       10.13        36.99         7.59        27.25        34.29        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.95         0.36        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       14.01        13.45         4.24         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       19.89        31.69        64.60        63.52        43.79         5.95 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        6.35        10.09        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59        31.23        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  DSC2 MUTATED DSC2 WILD-TYPE 
          0.13           0.00 
  DSC2 MUTATED DSC2 WILD-TYPE 
         53.29         238.29 
  DSC2 MUTATED DSC2 WILD-TYPE 
         12.28          19.89 
[1] "0.1 - 53.3 (12.3)"  "0.0 - 238.3 (19.9)"
[1] "hr=" "1.5"
D64V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DSC2 MUTATED         0        2        8         4         1          5
  DSC2 WILD-TYPE       4      121      124        43        65         65
                vv
clus             STAGE IIIB STAGE IV
  DSC2 MUTATED            0        0
  DSC2 WILD-TYPE         11       25
D64V3, multiclass
            clus
vv           DSC2 MUTATED DSC2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            121
  STAGE IB              8            124
  STAGE IIA             4             43
  STAGE IIB             1             65
  STAGE IIIA            5             65
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSC2 MUTATED     6  13   1   0
  DSC2 WILD-TYPE 149 248  42  18
D64V4, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  T1            6            149
  T2           13            248
  T3            1             42
  T4            0             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
  DSC2 MUTATED    10   4     5
  DSC2 WILD-TYPE 297  85    67
D64V5, multiclass
       clus
vv      DSC2 MUTATED DSC2 WILD-TYPE
  N0              10            297
  N1               4             85
  N2+N3            5             67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                cls
clus               0   1
  DSC2 MUTATED    14   0
  DSC2 WILD-TYPE 314  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     14    0
  DSC2 WILD-TYPE  314   23
   clus
vv  DSC2 MUTATED DSC2 WILD-TYPE
  0           14            314
  1            0             23
[1] 2 2
[1] FALSE
D64V7, binary
                cls
clus               0   1
  DSC2 MUTATED     9  11
  DSC2 WILD-TYPE 250 210
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED      9   11
  DSC2 WILD-TYPE  250  210
        clus
vv       DSC2 MUTATED DSC2 WILD-TYPE
  FEMALE            9            250
  MALE             11            210
[1] 2 2
[1] FALSE
D64V8, binary
                cls
clus               0   1
  DSC2 MUTATED    13   1
  DSC2 WILD-TYPE 320  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     13    1
  DSC2 WILD-TYPE  320   48
     clus
vv    DSC2 MUTATED DSC2 WILD-TYPE
  NO            13            320
  YES            1             48
[1] 2 2
[1] FALSE
D64V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DSC2 MUTATED                            1                                 3
  DSC2 WILD-TYPE                         17                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DSC2 MUTATED                                                    8
  DSC2 WILD-TYPE                                                287
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DSC2 MUTATED                                            0
  DSC2 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DSC2 MUTATED                                               2
  DSC2 WILD-TYPE                                            17
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  DSC2 MUTATED                                1
  DSC2 WILD-TYPE                              1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  DSC2 MUTATED                                    0
  DSC2 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DSC2 MUTATED                              0                             3
  DSC2 WILD-TYPE                            2                            19
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DSC2 MUTATED                                               0
  DSC2 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  DSC2 MUTATED                              2
  DSC2 WILD-TYPE                            7
D64V10, multiclass
                                                    clus
vv                                                   DSC2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 2
  LUNG CLEAR CELL ADENOCARCINOMA                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 3
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  2
                                                    clus
vv                                                   DSC2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  17
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  19
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
D64V12, continuous
                vv
clus              R0  R1  R2  RX
  DSC2 MUTATED    13   0   0   1
  DSC2 WILD-TYPE 297  11   4  24
D64V13, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  R0           13            297
  R1            0             11
  R2            0              4
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSC2 MUTATED                                  0     0
  DSC2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSC2 MUTATED                           3    15
  DSC2 WILD-TYPE                        26   362
D64V14, multiclass
                                  clus
vv                                 DSC2 MUTATED DSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   3             26
  WHITE                                      15            362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V15, binary
                cls
clus               0   1
  DSC2 MUTATED     1  14
  DSC2 WILD-TYPE   5 335
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED      1   14
  DSC2 WILD-TYPE    5  335
                        clus
vv                       DSC2 MUTATED DSC2 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           14            335
[1] 2 2
[1] FALSE

Clustering(65) Variable = RNF160 MUTATION ANALYSIS
D65V1, survival
                  sevent
clus2                0   1
  RNF160 MUTATED     9   6
  RNF160 WILD-TYPE 293 149
  RNF160 MUTATED RNF160 WILD-TYPE 
              15              442 
  RNF160 MUTATED RNF160 WILD-TYPE 
               6              149 
$`RNF160 MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-35-5375 TCGA-44-8117 TCGA-53-7624 TCGA-55-8090 
       19.96        37.02         8.68        12.66        34.29        19.66 
TCGA-67-3771 TCGA-86-8673 TCGA-86-A4JF TCGA-95-7567 TCGA-97-7554 TCGA-97-8174 
       20.05        28.34        24.23        18.67        25.48         5.39 
TCGA-MN-A4N4 TCGA-MP-A4TC TCGA-MP-A4TF 
       38.63         2.43        11.05 

$`RNF160 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        45.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.00        29.23        13.74         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       27.25        30.54        13.94        35.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19         3.29        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       28.47        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58         0.62        26.50        29.46 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
       17.29        41.82        16.54         2.86        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       31.69        64.60        63.52        43.79         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.72        18.67        17.92        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       10.09        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       31.23        10.09        29.46        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  RNF160 MUTATED RNF160 WILD-TYPE 
            2.43             0.00 
  RNF160 MUTATED RNF160 WILD-TYPE 
           38.63           238.29 
  RNF160 MUTATED RNF160 WILD-TYPE 
           19.96            19.79 
[1] "2.4 - 38.6 (20.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.6"
D65V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RNF160 MUTATED         0        3        4         2         2          3
  RNF160 WILD-TYPE       4      120      128        45        64         67
                  vv
clus               STAGE IIIB STAGE IV
  RNF160 MUTATED            0        1
  RNF160 WILD-TYPE         11       24
D65V3, multiclass
            clus
vv           RNF160 MUTATED RNF160 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                4              128
  STAGE IIA               2               45
  STAGE IIB               2               64
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                1               24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF160 MUTATED     4  10   1   0
  RNF160 WILD-TYPE 151 251  42  18
D65V4, multiclass
    clus
vv   RNF160 MUTATED RNF160 WILD-TYPE
  T1              4              151
  T2             10              251
  T3              1               42
  T4              0               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
  RNF160 MUTATED    11   1     3
  RNF160 WILD-TYPE 296  88    69
D65V5, multiclass
       clus
vv      RNF160 MUTATED RNF160 WILD-TYPE
  N0                11              296
  N1                 1               88
  N2+N3              3               69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                  cls
clus                 0   1
  RNF160 MUTATED    14   1
  RNF160 WILD-TYPE 314  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED     14    1
  RNF160 WILD-TYPE  314   22
   clus
vv  RNF160 MUTATED RNF160 WILD-TYPE
  0             14              314
  1              1               22
[1] 2 2
[1] FALSE
D65V7, binary
                  cls
clus                 0   1
  RNF160 MUTATED     6   9
  RNF160 WILD-TYPE 253 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED      6    9
  RNF160 WILD-TYPE  253  212
        clus
vv       RNF160 MUTATED RNF160 WILD-TYPE
  FEMALE              6              253
  MALE                9              212
[1] 2 2
[1] FALSE
D65V8, binary
                  cls
clus                 0   1
  RNF160 MUTATED    12   0
  RNF160 WILD-TYPE 321  49
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED     12    0
  RNF160 WILD-TYPE  321   49
     clus
vv    RNF160 MUTATED RNF160 WILD-TYPE
  NO              12              321
  YES              0               49
[1] 2 2
[1] FALSE
D65V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RNF160 MUTATED                            0                                 3
  RNF160 WILD-TYPE                         18                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RNF160 MUTATED                                                    9
  RNF160 WILD-TYPE                                                286
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RNF160 MUTATED                                            0
  RNF160 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RNF160 MUTATED                                               1
  RNF160 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  RNF160 MUTATED                                0
  RNF160 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  RNF160 MUTATED                                    0
  RNF160 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RNF160 MUTATED                              0                             2
  RNF160 WILD-TYPE                            2                            20
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RNF160 MUTATED                                               0
  RNF160 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  RNF160 MUTATED                              0
  RNF160 WILD-TYPE                            9
D65V10, multiclass
                                                    clus
vv                                                   RNF160 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   RNF160 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
D65V12, continuous
                  vv
clus                R0  R1  R2  RX
  RNF160 MUTATED    12   0   0   0
  RNF160 WILD-TYPE 298  11   4  25
D65V13, multiclass
    clus
vv   RNF160 MUTATED RNF160 WILD-TYPE
  R0             12              298
  R1              0               11
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF160 MUTATED                                  0     0
  RNF160 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF160 MUTATED                           1    12
  RNF160 WILD-TYPE                        28   365
D65V14, multiclass
                                  clus
vv                                 RNF160 MUTATED RNF160 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        12              365
[1] 4 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
  RNF160 MUTATED     1  12
  RNF160 WILD-TYPE   5 337
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED      1   12
  RNF160 WILD-TYPE    5  337
                        clus
vv                       RNF160 MUTATED RNF160 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             12              337
[1] 2 2
[1] FALSE

Clustering(66) Variable = AIFM1 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  AIFM1 MUTATED     7   4
  AIFM1 WILD-TYPE 295 151
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             11             446 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
              4             151 
$`AIFM1 MUTATED`
TCGA-38-4631 TCGA-44-6774 TCGA-50-6594 TCGA-55-8506 TCGA-55-A48X TCGA-55-A494 
       11.64        21.63        12.16         0.36        22.65        15.81 
TCGA-69-7974 TCGA-86-A456 TCGA-86-A4P7 TCGA-95-7043 TCGA-97-7938 
        6.05        29.46        13.64        16.54         0.59 

$`AIFM1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
      120.79        37.71        49.05        28.41        35.28        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       27.78        23.15        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.61         2.17        16.93        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       20.58        19.59         0.92        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       24.23        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29        41.82         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        6.35        10.09        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  AIFM1 MUTATED AIFM1 WILD-TYPE 
           0.36            0.00 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
          29.46          238.29 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
         13.640          19.855 
[1] "0.4 - 29.5 (13.6)"  "0.0 - 238.3 (19.9)"
[1] "hr=" "2.3"
D66V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  AIFM1 MUTATED         0        3        4         1         1          3
  AIFM1 WILD-TYPE       4      120      128        46        65         67
                 vv
clus              STAGE IIIB STAGE IV
  AIFM1 MUTATED            0        0
  AIFM1 WILD-TYPE         11       25
D66V3, multiclass
            clus
vv           AIFM1 MUTATED AIFM1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             120
  STAGE IB               4             128
  STAGE IIA              1              46
  STAGE IIB              1              65
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AIFM1 MUTATED     5   5   2   0
  AIFM1 WILD-TYPE 150 256  41  18
D66V4, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  T1             5             150
  T2             5             256
  T3             2              41
  T4             0              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
  AIFM1 MUTATED     8   1     3
  AIFM1 WILD-TYPE 299  88    69
D66V5, multiclass
       clus
vv      AIFM1 MUTATED AIFM1 WILD-TYPE
  N0                8             299
  N1                1              88
  N2+N3             3              69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                 cls
clus                0   1
  AIFM1 MUTATED     7   0
  AIFM1 WILD-TYPE 321  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      7    0
  AIFM1 WILD-TYPE  321   23
   clus
vv  AIFM1 MUTATED AIFM1 WILD-TYPE
  0             7             321
  1             0              23
[1] 2 2
[1] FALSE
D66V7, binary
                 cls
clus                0   1
  AIFM1 MUTATED    12   0
  AIFM1 WILD-TYPE 247 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED     12    0
  AIFM1 WILD-TYPE  247  221
        clus
vv       AIFM1 MUTATED AIFM1 WILD-TYPE
  FEMALE            12             247
  MALE               0             221
[1] 2 2
[1] FALSE
D66V8, binary
                 cls
clus                0   1
  AIFM1 MUTATED     9   2
  AIFM1 WILD-TYPE 324  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      9    2
  AIFM1 WILD-TYPE  324   47
     clus
vv    AIFM1 MUTATED AIFM1 WILD-TYPE
  NO              9             324
  YES             2              47
[1] 2 2
[1] FALSE
D66V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  AIFM1 MUTATED                            0                                 2
  AIFM1 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AIFM1 MUTATED                                                    8
  AIFM1 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AIFM1 MUTATED                                            0
  AIFM1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AIFM1 MUTATED                                               1
  AIFM1 WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  AIFM1 MUTATED                                0
  AIFM1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  AIFM1 MUTATED                                    0
  AIFM1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  AIFM1 MUTATED                              0                             1
  AIFM1 WILD-TYPE                            2                            21
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AIFM1 MUTATED                                               0
  AIFM1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  AIFM1 MUTATED                              0
  AIFM1 WILD-TYPE                            9
D66V10, multiclass
                                                    clus
vv                                                   AIFM1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   AIFM1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
D66V12, continuous
                 vv
clus               R0  R1  R2  RX
  AIFM1 MUTATED     8   0   0   0
  AIFM1 WILD-TYPE 302  11   4  25
D66V13, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  R0             8             302
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AIFM1 MUTATED                                  0     1
  AIFM1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AIFM1 MUTATED                           1     9
  AIFM1 WILD-TYPE                        28   368
D66V14, multiclass
                                  clus
vv                                 AIFM1 MUTATED AIFM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        9             368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V15, binary
                 cls
clus                0   1
  AIFM1 MUTATED     0  11
  AIFM1 WILD-TYPE   6 338
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      0   11
  AIFM1 WILD-TYPE    6  338
                        clus
vv                       AIFM1 MUTATED AIFM1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            11             338
[1] 2 2
[1] FALSE

Clustering(67) Variable = DOT1L MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2               0   1
  DOT1L MUTATED     9   4
  DOT1L WILD-TYPE 293 151
  DOT1L MUTATED DOT1L WILD-TYPE 
             13             444 
  DOT1L MUTATED DOT1L WILD-TYPE 
              4             151 
$`DOT1L MUTATED`
TCGA-05-4384 TCGA-49-4486 TCGA-49-6767 TCGA-50-5072 TCGA-53-7624 TCGA-55-7727 
       14.01        76.21        22.26         8.09        34.29         1.12 
TCGA-55-8511 TCGA-62-8395 TCGA-64-5781 TCGA-69-7974 TCGA-78-7156 TCGA-86-A4JF 
        0.30        39.98        51.25         6.05        32.09        24.23 
TCGA-91-6836 
       13.71 

$`DOT1L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        13.45        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       11.64        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       27.25        30.54        13.94        35.21        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.28         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.26         0.49        17.72         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 
        0.92        15.81        20.19        19.99         4.57        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
        6.12        22.68        13.61         5.42         7.56         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       50.33       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       28.34        26.50        29.46        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  DOT1L MUTATED DOT1L WILD-TYPE 
            0.3             0.0 
  DOT1L MUTATED DOT1L WILD-TYPE 
          76.21          238.29 
  DOT1L MUTATED DOT1L WILD-TYPE 
          22.26           19.79 
[1] "0.3 - 76.2 (22.3)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.1"
D67V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DOT1L MUTATED         0        1        4         0         3          4
  DOT1L WILD-TYPE       4      122      128        47        63         66
                 vv
clus              STAGE IIIB STAGE IV
  DOT1L MUTATED            0        2
  DOT1L WILD-TYPE         11       23
D67V3, multiclass
            clus
vv           DOT1L MUTATED DOT1L WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               4             128
  STAGE IIA              0              47
  STAGE IIB              3              63
  STAGE IIIA             4              66
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DOT1L MUTATED     2   8   3   1
  DOT1L WILD-TYPE 153 253  40  17
D67V4, multiclass
    clus
vv   DOT1L MUTATED DOT1L WILD-TYPE
  T1             2             153
  T2             8             253
  T3             3              40
  T4             1              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
  DOT1L MUTATED     9   1     4
  DOT1L WILD-TYPE 298  88    68
D67V5, multiclass
       clus
vv      DOT1L MUTATED DOT1L WILD-TYPE
  N0                9             298
  N1                1              88
  N2+N3             4              68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                 cls
clus                0   1
  DOT1L MUTATED     7   2
  DOT1L WILD-TYPE 321  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      7    2
  DOT1L WILD-TYPE  321   21
   clus
vv  DOT1L MUTATED DOT1L WILD-TYPE
  0             7             321
  1             2              21
[1] 2 2
[1] FALSE
D67V7, binary
                 cls
clus                0   1
  DOT1L MUTATED     7   7
  DOT1L WILD-TYPE 252 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      7    7
  DOT1L WILD-TYPE  252  214
        clus
vv       DOT1L MUTATED DOT1L WILD-TYPE
  FEMALE             7             252
  MALE               7             214
[1] 2 2
[1] FALSE
D67V8, binary
                 cls
clus                0   1
  DOT1L MUTATED     8   2
  DOT1L WILD-TYPE 325  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      8    2
  DOT1L WILD-TYPE  325   47
     clus
vv    DOT1L MUTATED DOT1L WILD-TYPE
  NO              8             325
  YES             2              47
[1] 2 2
[1] FALSE
D67V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DOT1L MUTATED                            0                                 6
  DOT1L WILD-TYPE                         18                                95
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DOT1L MUTATED                                                    8
  DOT1L WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DOT1L MUTATED                                            0
  DOT1L WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DOT1L MUTATED                                               0
  DOT1L WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  DOT1L MUTATED                                0
  DOT1L WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  DOT1L MUTATED                                    0
  DOT1L WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DOT1L MUTATED                              0                             0
  DOT1L WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DOT1L MUTATED                                               0
  DOT1L WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  DOT1L MUTATED                              0
  DOT1L WILD-TYPE                            9
D67V10, multiclass
                                                    clus
vv                                                   DOT1L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   DOT1L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
D67V12, continuous
                 vv
clus               R0  R1  R2  RX
  DOT1L MUTATED     9   0   0   2
  DOT1L WILD-TYPE 301  11   4  23
D67V13, multiclass
    clus
vv   DOT1L MUTATED DOT1L WILD-TYPE
  R0             9             301
  R1             0              11
  R2             0               4
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOT1L MUTATED                                  0     0
  DOT1L WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DOT1L MUTATED                           0    12
  DOT1L WILD-TYPE                        29   365
D67V14, multiclass
                                  clus
vv                                 DOT1L MUTATED DOT1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       12             365
[1] 4 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
  DOT1L MUTATED     1   9
  DOT1L WILD-TYPE   5 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      1    9
  DOT1L WILD-TYPE    5  340
                        clus
vv                       DOT1L MUTATED DOT1L WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             9             340
[1] 2 2
[1] FALSE

Clustering(68) Variable = MCM9 MUTATION ANALYSIS
D68V1, survival
                sevent
clus2              0   1
  MCM9 MUTATED     2   1
  MCM9 WILD-TYPE 300 154
  MCM9 MUTATED MCM9 WILD-TYPE 
             3            454 
  MCM9 MUTATED MCM9 WILD-TYPE 
             1            154 
$`MCM9 MUTATED`
TCGA-38-4625 TCGA-49-4486 TCGA-69-7979 
       97.74        76.21         2.93 

$`MCM9 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
        9.04         2.04         7.40         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        13.45        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  MCM9 MUTATED MCM9 WILD-TYPE 
          2.93           0.00 
  MCM9 MUTATED MCM9 WILD-TYPE 
         97.74         238.29 
  MCM9 MUTATED MCM9 WILD-TYPE 
         76.21          19.79 
[1] "2.9 - 97.7 (76.2)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "2.7"
D68V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MCM9 MUTATED         0        1        2         0         0          0
  MCM9 WILD-TYPE       4      122      130        47        66         70
                vv
clus             STAGE IIIB STAGE IV
  MCM9 MUTATED            0        0
  MCM9 WILD-TYPE         11       25
D68V3, multiclass
            clus
vv           MCM9 MUTATED MCM9 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              2            130
  STAGE IIA             0             47
  STAGE IIB             0             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MCM9 MUTATED     1   2   0   0
  MCM9 WILD-TYPE 154 259  43  18
D68V4, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  T1            1            154
  T2            2            259
  T3            0             43
  T4            0             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
  MCM9 MUTATED     3   0     0
  MCM9 WILD-TYPE 304  89    72
D68V5, multiclass
       clus
vv      MCM9 MUTATED MCM9 WILD-TYPE
  N0               3            304
  N1               0             89
  N2+N3            0             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                cls
clus               0   1
  MCM9 MUTATED     2   0
  MCM9 WILD-TYPE 326  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      2    0
  MCM9 WILD-TYPE  326   23
   clus
vv  MCM9 MUTATED MCM9 WILD-TYPE
  0            2            326
  1            0             23
[1] 2 2
[1] FALSE
D68V7, binary
                cls
clus               0   1
  MCM9 MUTATED     2   1
  MCM9 WILD-TYPE 257 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      2    1
  MCM9 WILD-TYPE  257  220
        clus
vv       MCM9 MUTATED MCM9 WILD-TYPE
  FEMALE            2            257
  MALE              1            220
[1] 2 2
[1] FALSE
D68V8, binary
                cls
clus               0   1
  MCM9 MUTATED     2   0
  MCM9 WILD-TYPE 331  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      2    0
  MCM9 WILD-TYPE  331   49
     clus
vv    MCM9 MUTATED MCM9 WILD-TYPE
  NO             2            331
  YES            0             49
[1] 2 2
[1] FALSE
D68V9, continuous
[1] "Remove cluster labels:" "MCM9 MUTATED"          
clus
  MCM9 MUTATED MCM9 WILD-TYPE 
             1            116 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-44-3396 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-6144     TCGA-44-6147 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-44-A47F     TCGA-49-4494 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4510     TCGA-49-6742 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-6743     TCGA-49-6744     TCGA-53-7624     TCGA-53-A4EZ 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7573     TCGA-55-7725     TCGA-55-7910 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8089     TCGA-55-8096     TCGA-55-8205 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8208     TCGA-55-8507     TCGA-55-8508     TCGA-55-8511 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8619     TCGA-55-8620     TCGA-55-8621 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8394     TCGA-62-8395     TCGA-62-8397 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-8398     TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-A472     TCGA-64-1677     TCGA-64-1681     TCGA-64-5775 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4662     TCGA-73-4666 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4676     TCGA-73-4677 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-73-7498     TCGA-73-7499     TCGA-75-5122     TCGA-83-5908 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-6562     TCGA-86-6851     TCGA-86-7701     TCGA-86-7711 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7953     TCGA-86-7954 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-7955     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8280     TCGA-86-8281 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6849     TCGA-93-7347     TCGA-93-7348 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-95-7567 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-99-7458     TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MCM9 MUTATED                            1                                 0
  MCM9 WILD-TYPE                         17                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MCM9 MUTATED                                                    2
  MCM9 WILD-TYPE                                                293
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MCM9 MUTATED                                            0
  MCM9 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MCM9 MUTATED                                               0
  MCM9 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  MCM9 MUTATED                                0
  MCM9 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  MCM9 MUTATED                                    0
  MCM9 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MCM9 MUTATED                              0                             0
  MCM9 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MCM9 MUTATED                                               0
  MCM9 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  MCM9 MUTATED                              0
  MCM9 WILD-TYPE                            9
D68V10, multiclass
                                                    clus
vv                                                   MCM9 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   MCM9 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
D68V12, continuous
                vv
clus              R0  R1  R2  RX
  MCM9 MUTATED     2   0   0   0
  MCM9 WILD-TYPE 308  11   4  25
D68V13, multiclass
[1] "Remove cluster labels:" "MCM9 MUTATED"          
clus
  MCM9 MUTATED MCM9 WILD-TYPE 
             2            348 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4382 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4384     TCGA-05-4389     TCGA-05-4390     TCGA-05-4395 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4396     TCGA-05-4397     TCGA-05-4398     TCGA-05-4402 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4405     TCGA-05-4410     TCGA-05-4415 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4418     TCGA-05-4420     TCGA-05-4422 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4424     TCGA-05-4425     TCGA-05-4426     TCGA-05-4427 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-4434 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-5420     TCGA-05-5423     TCGA-05-5425     TCGA-05-5428 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-5429     TCGA-05-5715     TCGA-35-4122     TCGA-35-4123 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-35-5375     TCGA-38-4626     TCGA-38-4627     TCGA-38-4628 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-38-4629     TCGA-38-4630     TCGA-38-4631     TCGA-38-4632 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-38-6178     TCGA-38-7271     TCGA-38-A44F     TCGA-44-2657 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-2661     TCGA-44-2665     TCGA-44-3396     TCGA-44-3398 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-3919     TCGA-44-4112     TCGA-44-6144 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6775     TCGA-44-A479     TCGA-44-A47A 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47G     TCGA-44-A4SU     TCGA-49-4487 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-4488     TCGA-49-4494     TCGA-49-4501     TCGA-49-4505 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-4506     TCGA-49-4507     TCGA-49-4510     TCGA-49-4512 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-4514     TCGA-49-6742     TCGA-49-6744     TCGA-49-6761 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-6767     TCGA-50-5051     TCGA-50-5055     TCGA-50-5066 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-50-5931     TCGA-50-5942     TCGA-50-5944     TCGA-50-6593 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-50-6597     TCGA-50-6673     TCGA-50-8460     TCGA-53-7624 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-53-7626     TCGA-53-A4EZ     TCGA-55-1592     TCGA-55-5899 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-6642     TCGA-55-6970     TCGA-55-6971     TCGA-55-6972 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-6980     TCGA-55-6981     TCGA-55-6983     TCGA-55-6985 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7281     TCGA-55-7284     TCGA-55-7570     TCGA-55-7574 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7576     TCGA-55-7724     TCGA-55-7725     TCGA-55-7726 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7727     TCGA-55-7728     TCGA-55-7815     TCGA-55-7903 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7907     TCGA-55-7910     TCGA-55-7911     TCGA-55-7914 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7994     TCGA-55-7995     TCGA-55-8085     TCGA-55-8087 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8090     TCGA-55-8091     TCGA-55-8092 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8097     TCGA-55-8203     TCGA-55-8204 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8206     TCGA-55-8207     TCGA-55-8208 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8505 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8506     TCGA-55-8507     TCGA-55-8508     TCGA-55-8510 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8513     TCGA-55-8514 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8614     TCGA-55-8615     TCGA-55-8616     TCGA-55-8619 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8620     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A48Y 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491     TCGA-55-A492 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DF     TCGA-55-A4DG 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-8394     TCGA-62-8395     TCGA-62-8397     TCGA-62-8398 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-64-1676     TCGA-64-1677     TCGA-64-1679     TCGA-64-1681 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-64-5774     TCGA-64-5775     TCGA-64-5778     TCGA-64-5779 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-64-5781     TCGA-64-5815     TCGA-67-3771     TCGA-67-3773 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-67-4679     TCGA-67-6215     TCGA-67-6216     TCGA-67-6217 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4658     TCGA-73-4659 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-73-4662     TCGA-73-4666     TCGA-73-4668     TCGA-73-4670 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-73-4677     TCGA-73-7498 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-73-7499     TCGA-75-5122     TCGA-75-5125     TCGA-75-5126 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-75-5146     TCGA-75-5147     TCGA-75-6203     TCGA-75-6205 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-75-6206     TCGA-75-6207     TCGA-75-6211     TCGA-75-6212 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-75-6214     TCGA-75-7025     TCGA-75-7027     TCGA-75-7030 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-75-7031     TCGA-78-7143     TCGA-78-7145     TCGA-78-7146 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7147     TCGA-78-7148     TCGA-78-7149     TCGA-78-7150 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7152     TCGA-78-7153     TCGA-78-7154     TCGA-78-7155 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7156     TCGA-78-7158     TCGA-78-7159     TCGA-78-7160 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7161     TCGA-78-7162     TCGA-78-7163     TCGA-78-7166 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7167     TCGA-78-7220     TCGA-78-7535     TCGA-78-7536 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7537     TCGA-78-7539     TCGA-78-7540     TCGA-78-7542 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8640     TCGA-78-8648     TCGA-78-8655 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-8660     TCGA-78-8662     TCGA-80-5607     TCGA-80-5608 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-80-5611     TCGA-83-5908     TCGA-86-6562     TCGA-86-7701 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-7711     TCGA-86-7713     TCGA-86-7714     TCGA-86-7953 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-7955     TCGA-86-8054     TCGA-86-8055 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8056     TCGA-86-8073     TCGA-86-8074     TCGA-86-8075 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8076     TCGA-86-8278     TCGA-86-8279     TCGA-86-8280 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8585     TCGA-86-8668 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8671     TCGA-86-8672     TCGA-86-8673 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-91-6828     TCGA-91-6829     TCGA-91-6835     TCGA-91-6840 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-91-A4BD     TCGA-93-7347     TCGA-93-7348     TCGA-93-8067 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JP     TCGA-93-A4JQ 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7944     TCGA-95-7947     TCGA-95-7948 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-95-8039     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-97-7546 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-97-7554     TCGA-97-7938     TCGA-97-7941     TCGA-97-8176 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M7     TCGA-99-7458     TCGA-99-8025 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-99-8028     TCGA-99-8032     TCGA-99-8033     TCGA-J2-A4AD 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-J2-A4AE     TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MN-A4N4 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MN-A4N5     TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4T2     TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4T8     TCGA-MP-A4T9     TCGA-MP-A4TA     TCGA-MP-A4TC 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4TD     TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4TI     TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YQ 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCM9 MUTATED                                  0     0
  MCM9 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MCM9 MUTATED                           0     3
  MCM9 WILD-TYPE                        29   374
D68V14, multiclass
                                  clus
vv                                 MCM9 MUTATED MCM9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       3            374
[1] 4 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
  MCM9 MUTATED     0   3
  MCM9 WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      0    3
  MCM9 WILD-TYPE    6  346
                        clus
vv                       MCM9 MUTATED MCM9 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            346
[1] 2 2
[1] FALSE

Clustering(69) Variable = NCKAP1L MUTATION ANALYSIS
D69V1, survival
                   sevent
clus2                 0   1
  NCKAP1L MUTATED    11   8
  NCKAP1L WILD-TYPE 291 147
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
               19               438 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                8               147 
$`NCKAP1L MUTATED`
TCGA-05-4396 TCGA-05-4432 TCGA-44-7667 TCGA-44-7670 TCGA-50-5930 TCGA-50-5946 
        9.96        25.02        36.07        29.00         9.27        22.55 
TCGA-55-1592 TCGA-55-7907 TCGA-55-8092 TCGA-67-3771 TCGA-73-4658 TCGA-78-7162 
       23.05         0.53         5.06        20.05        52.60       104.19 
TCGA-78-7536 TCGA-78-7633 TCGA-95-7039 TCGA-95-A4VK TCGA-99-8028 TCGA-L9-A444 
        8.02        50.24        41.82        21.40        36.76        10.09 
TCGA-MN-A4N4 
       38.63 

$`NCKAP1L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
       16.44        22.72        19.46        12.03         7.17        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.23        13.74        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.09        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
        8.45        15.12         9.37        29.03        25.12        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       30.54        13.94        35.21        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78         1.45        18.64         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01         6.90        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 
        5.88        64.90        22.92         9.57       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53        31.20        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       10.55       232.18        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP 
       15.68        15.65        27.29         2.76        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        24.56        34.85         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        6.35        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
             0.53              0.00 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
           104.19            238.29 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
           23.050            19.625 
[1] "0.5 - 104.2 (23.1)" "0.0 - 238.3 (19.6)"
[1] "hr=" "1.1"
D69V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NCKAP1L MUTATED         0        7        2         2         4          3
  NCKAP1L WILD-TYPE       4      116      130        45        62         67
                   vv
clus                STAGE IIIB STAGE IV
  NCKAP1L MUTATED            1        0
  NCKAP1L WILD-TYPE         10       25
D69V3, multiclass
            clus
vv           NCKAP1L MUTATED NCKAP1L WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 7               116
  STAGE IB                 2               130
  STAGE IIA                2                45
  STAGE IIB                4                62
  STAGE IIIA               3                67
  STAGE IIIB               1                10
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  NCKAP1L MUTATED     7   8   3   1
  NCKAP1L WILD-TYPE 148 253  40  17
D69V4, multiclass
    clus
vv   NCKAP1L MUTATED NCKAP1L WILD-TYPE
  T1               7               148
  T2               8               253
  T3               3                40
  T4               1                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
  NCKAP1L MUTATED    12   4     3
  NCKAP1L WILD-TYPE 295  85    69
D69V5, multiclass
       clus
vv      NCKAP1L MUTATED NCKAP1L WILD-TYPE
  N0                 12               295
  N1                  4                85
  N2+N3               3                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED    13   0
  NCKAP1L WILD-TYPE 315  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED     13    0
  NCKAP1L WILD-TYPE  315   23
   clus
vv  NCKAP1L MUTATED NCKAP1L WILD-TYPE
  0              13               315
  1               0                23
[1] 2 2
[1] FALSE
D69V7, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED     8  11
  NCKAP1L WILD-TYPE 251 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED      8   11
  NCKAP1L WILD-TYPE  251  210
        clus
vv       NCKAP1L MUTATED NCKAP1L WILD-TYPE
  FEMALE               8               251
  MALE                11               210
[1] 2 2
[1] FALSE
D69V8, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED    12   3
  NCKAP1L WILD-TYPE 321  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED     12    3
  NCKAP1L WILD-TYPE  321   46
     clus
vv    NCKAP1L MUTATED NCKAP1L WILD-TYPE
  NO               12               321
  YES               3                46
[1] 2 2
[1] FALSE
D69V9, continuous
[1] "Remove cluster labels:" "NCKAP1L MUTATED"       
clus
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                1               116 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-44-3396 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-44-3918        TCGA-44-4112        TCGA-44-6144        TCGA-44-6147 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-44-6775        TCGA-44-7660        TCGA-44-A47F        TCGA-49-4486 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-49-4494        TCGA-49-4505        TCGA-49-4506        TCGA-49-4510 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-49-6742        TCGA-49-6743        TCGA-49-6744        TCGA-53-7624 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-53-A4EZ        TCGA-55-7283        TCGA-55-7573        TCGA-55-7725 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-7910        TCGA-55-7914        TCGA-55-8089        TCGA-55-8096 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-8205        TCGA-55-8208        TCGA-55-8507        TCGA-55-8508 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-8511        TCGA-55-8512        TCGA-55-8619        TCGA-55-8620 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-8621        TCGA-55-A48Z        TCGA-55-A490        TCGA-55-A491 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-A492        TCGA-55-A494        TCGA-62-8394        TCGA-62-8395 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-8397        TCGA-62-8398        TCGA-62-8399        TCGA-62-8402 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-A471        TCGA-62-A472        TCGA-64-1677        TCGA-64-1681 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-64-5775        TCGA-64-5778        TCGA-69-7974        TCGA-69-8254 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-71-6725        TCGA-71-8520        TCGA-73-4659        TCGA-73-4662 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-73-4666        TCGA-73-4668        TCGA-73-4670        TCGA-73-4676 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-73-4677        TCGA-73-7498        TCGA-73-7499        TCGA-75-5122 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-83-5908        TCGA-86-6562        TCGA-86-6851        TCGA-86-7701 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-7711        TCGA-86-7713        TCGA-86-7714        TCGA-86-7953 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-7954        TCGA-86-7955        TCGA-86-8054        TCGA-86-8055 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8073        TCGA-86-8074        TCGA-86-8075 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8076        TCGA-86-8278        TCGA-86-8279        TCGA-86-8280 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8281        TCGA-86-8358        TCGA-86-8359        TCGA-86-8668 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8669        TCGA-86-8671        TCGA-86-A456        TCGA-86-A4JF 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-A4P7        TCGA-91-6829        TCGA-91-6849        TCGA-93-7347 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-93-7348        TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-95-7567        TCGA-99-7458        TCGA-MN-A4N1        TCGA-MN-A4N5 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  NCKAP1L MUTATED                            0
  NCKAP1L WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  NCKAP1L MUTATED                                   7
  NCKAP1L WILD-TYPE                                94
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NCKAP1L MUTATED                                                   12
  NCKAP1L WILD-TYPE                                                283
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  NCKAP1L MUTATED                                            0
  NCKAP1L WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  NCKAP1L MUTATED                                               0
  NCKAP1L WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  NCKAP1L MUTATED                                0
  NCKAP1L WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  NCKAP1L MUTATED                                    0
  NCKAP1L WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  NCKAP1L MUTATED                              0                             0
  NCKAP1L WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  NCKAP1L MUTATED                                               0
  NCKAP1L WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  NCKAP1L MUTATED                              0
  NCKAP1L WILD-TYPE                            9
D69V10, multiclass
                                                    clus
vv                                                   NCKAP1L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   NCKAP1L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, continuous
D69V12, continuous
                   vv
clus                 R0  R1  R2  RX
  NCKAP1L MUTATED    13   0   0   1
  NCKAP1L WILD-TYPE 297  11   4  24
D69V13, multiclass
    clus
vv   NCKAP1L MUTATED NCKAP1L WILD-TYPE
  R0              13               297
  R1               0                11
  R2               0                 4
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCKAP1L MUTATED                                  0     0
  NCKAP1L WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  NCKAP1L MUTATED                           2    15
  NCKAP1L WILD-TYPE                        27   362
D69V14, multiclass
                                  clus
vv                                 NCKAP1L MUTATED NCKAP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                27
  WHITE                                         15               362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V15, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED     1  12
  NCKAP1L WILD-TYPE   5 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED      1   12
  NCKAP1L WILD-TYPE    5  337
                        clus
vv                       NCKAP1L MUTATED NCKAP1L WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              12               337
[1] 2 2
[1] FALSE

Clustering(70) Variable = ESYT3 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2               0   1
  ESYT3 MUTATED     6   2
  ESYT3 WILD-TYPE 296 153
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              8             449 
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              2             153 
$`ESYT3 MUTATED`
TCGA-05-4397 TCGA-05-5425 TCGA-38-7271 TCGA-44-7661 TCGA-55-8089 TCGA-55-8506 
       24.03        29.00        26.30        12.03         3.29         0.36 
TCGA-62-A46U TCGA-91-6849 
       67.96         1.15 

$`ESYT3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       22.72        19.46         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.23        13.74        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        54.35        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        7.36        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29        41.82        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.57        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       32.48        19.00        14.30         6.35        10.09        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        59.11 

  ESYT3 MUTATED ESYT3 WILD-TYPE 
           0.36            0.00 
  ESYT3 MUTATED ESYT3 WILD-TYPE 
          67.96          238.29 
  ESYT3 MUTATED ESYT3 WILD-TYPE 
          18.03           19.82 
[1] "0.4 - 68.0 (18.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.1"
D70V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ESYT3 MUTATED         0        2        1         0         4          1
  ESYT3 WILD-TYPE       4      121      131        47        62         69
                 vv
clus              STAGE IIIB STAGE IV
  ESYT3 MUTATED            0        0
  ESYT3 WILD-TYPE         11       25
D70V3, multiclass
            clus
vv           ESYT3 MUTATED ESYT3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               1             131
  STAGE IIA              0              47
  STAGE IIB              4              62
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ESYT3 MUTATED     2   5   1   0
  ESYT3 WILD-TYPE 153 256  42  18
D70V4, multiclass
    clus
vv   ESYT3 MUTATED ESYT3 WILD-TYPE
  T1             2             153
  T2             5             256
  T3             1              42
  T4             0              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
  ESYT3 MUTATED     4   3     1
  ESYT3 WILD-TYPE 303  86    71
D70V5, multiclass
       clus
vv      ESYT3 MUTATED ESYT3 WILD-TYPE
  N0                4             303
  N1                3              86
  N2+N3             1              71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                 cls
clus                0   1
  ESYT3 MUTATED     6   0
  ESYT3 WILD-TYPE 322  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      6    0
  ESYT3 WILD-TYPE  322   23
   clus
vv  ESYT3 MUTATED ESYT3 WILD-TYPE
  0             6             322
  1             0              23
[1] 2 2
[1] FALSE
D70V7, binary
                 cls
clus                0   1
  ESYT3 MUTATED     5   3
  ESYT3 WILD-TYPE 254 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      5    3
  ESYT3 WILD-TYPE  254  218
        clus
vv       ESYT3 MUTATED ESYT3 WILD-TYPE
  FEMALE             5             254
  MALE               3             218
[1] 2 2
[1] FALSE
D70V8, binary
                 cls
clus                0   1
  ESYT3 MUTATED     3   1
  ESYT3 WILD-TYPE 330  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      3    1
  ESYT3 WILD-TYPE  330   48
     clus
vv    ESYT3 MUTATED ESYT3 WILD-TYPE
  NO              3             330
  YES             1              48
[1] 2 2
[1] FALSE
D70V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ESYT3 MUTATED                            0                                 3
  ESYT3 WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ESYT3 MUTATED                                                    5
  ESYT3 WILD-TYPE                                                290
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ESYT3 MUTATED                                            0
  ESYT3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ESYT3 MUTATED                                               0
  ESYT3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ESYT3 MUTATED                                0
  ESYT3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ESYT3 MUTATED                                    0
  ESYT3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ESYT3 MUTATED                              0                             0
  ESYT3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ESYT3 MUTATED                                               0
  ESYT3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ESYT3 MUTATED                              0
  ESYT3 WILD-TYPE                            9
D70V10, multiclass
                                                    clus
vv                                                   ESYT3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ESYT3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, continuous
D70V12, continuous
                 vv
clus               R0  R1  R2  RX
  ESYT3 MUTATED     6   0   0   0
  ESYT3 WILD-TYPE 304  11   4  25
D70V13, multiclass
    clus
vv   ESYT3 MUTATED ESYT3 WILD-TYPE
  R0             6             304
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESYT3 MUTATED                                  0     0
  ESYT3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESYT3 MUTATED                           1     5
  ESYT3 WILD-TYPE                        28   372
D70V14, multiclass
                                  clus
vv                                 ESYT3 MUTATED ESYT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V15, binary
                 cls
clus                0   1
  ESYT3 MUTATED     0   6
  ESYT3 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      0    6
  ESYT3 WILD-TYPE    6  343
                        clus
vv                       ESYT3 MUTATED ESYT3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(71) Variable = MIA2 MUTATION ANALYSIS
D71V1, survival
                sevent
clus2              0   1
  MIA2 MUTATED     8   5
  MIA2 WILD-TYPE 294 150
  MIA2 MUTATED MIA2 WILD-TYPE 
            13            444 
  MIA2 MUTATED MIA2 WILD-TYPE 
             5            150 
$`MIA2 MUTATED`
TCGA-05-4424 TCGA-38-4629 TCGA-38-4630 TCGA-50-5944 TCGA-55-5899 TCGA-55-8203 
       30.02        28.41        35.28        25.12         2.86        17.98 
TCGA-55-A4DG TCGA-78-7152 TCGA-78-7155 TCGA-86-6851 TCGA-91-6831 TCGA-91-7771 
       19.99        39.95        38.50         5.88        10.19        16.18 
TCGA-MP-A4TK 
       19.13 

$`MIA2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       37.71        49.05        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       48.62         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        0.13        23.64        15.65         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 
       19.59         0.92        15.81        20.19         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       13.45         4.24        17.16         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
        5.69        19.27        20.58       129.53        21.90       119.51 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62        41.36         1.97         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       24.36        14.10        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  MIA2 MUTATED MIA2 WILD-TYPE 
          2.86           0.00 
  MIA2 MUTATED MIA2 WILD-TYPE 
         39.95         238.29 
  MIA2 MUTATED MIA2 WILD-TYPE 
         19.99          19.79 
[1] "2.9 - 40.0 (20.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.4"
D71V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MIA2 MUTATED         0        4        4         1         4          0
  MIA2 WILD-TYPE       4      119      128        46        62         70
                vv
clus             STAGE IIIB STAGE IV
  MIA2 MUTATED            0        0
  MIA2 WILD-TYPE         11       25
D71V3, multiclass
            clus
vv           MIA2 MUTATED MIA2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              4            119
  STAGE IB              4            128
  STAGE IIA             1             46
  STAGE IIB             4             62
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MIA2 MUTATED     5   5   3   0
  MIA2 WILD-TYPE 150 256  40  18
D71V4, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  T1            5            150
  T2            5            256
  T3            3             40
  T4            0             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
  MIA2 MUTATED    10   3     0
  MIA2 WILD-TYPE 297  86    72
D71V5, multiclass
       clus
vv      MIA2 MUTATED MIA2 WILD-TYPE
  N0              10            297
  N1               3             86
  N2+N3            0             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                cls
clus               0   1
  MIA2 MUTATED     9   0
  MIA2 WILD-TYPE 319  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      9    0
  MIA2 WILD-TYPE  319   23
   clus
vv  MIA2 MUTATED MIA2 WILD-TYPE
  0            9            319
  1            0             23
[1] 2 2
[1] FALSE
D71V7, binary
                cls
clus               0   1
  MIA2 MUTATED     5   8
  MIA2 WILD-TYPE 254 213
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      5    8
  MIA2 WILD-TYPE  254  213
        clus
vv       MIA2 MUTATED MIA2 WILD-TYPE
  FEMALE            5            254
  MALE              8            213
[1] 2 2
[1] FALSE
D71V8, binary
                cls
clus               0   1
  MIA2 MUTATED     9   2
  MIA2 WILD-TYPE 324  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      9    2
  MIA2 WILD-TYPE  324   47
     clus
vv    MIA2 MUTATED MIA2 WILD-TYPE
  NO             9            324
  YES            2             47
[1] 2 2
[1] FALSE
D71V9, continuous
[1] "Remove cluster labels:" "MIA2 MUTATED"          
clus
  MIA2 MUTATED MIA2 WILD-TYPE 
             1            116 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-44-3396 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-6144     TCGA-44-6147 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-44-A47F     TCGA-49-4486 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-49-4494     TCGA-49-4505     TCGA-49-4506     TCGA-49-4510 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-49-6742     TCGA-49-6743     TCGA-49-6744     TCGA-53-7624 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-53-A4EZ     TCGA-55-7283     TCGA-55-7573     TCGA-55-7725 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7914     TCGA-55-8089     TCGA-55-8096 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-8205     TCGA-55-8208     TCGA-55-8507     TCGA-55-8508 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8512     TCGA-55-8619     TCGA-55-8620 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-8621     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A491 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A494     TCGA-62-8394     TCGA-62-8395 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-62-8397     TCGA-62-8398     TCGA-62-8399     TCGA-62-8402 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1677     TCGA-64-1681 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-69-7974     TCGA-69-8254 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4659     TCGA-73-4662 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-73-4666     TCGA-73-4668     TCGA-73-4670     TCGA-73-4676 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-73-4677     TCGA-73-7498     TCGA-73-7499     TCGA-75-5122 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6562     TCGA-86-7701     TCGA-86-7711 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7953     TCGA-86-7954 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-7955     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8280     TCGA-86-8281 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6849     TCGA-93-7347     TCGA-93-7348 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-95-7567 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-99-7458     TCGA-MN-A4N1     TCGA-MN-A4N4     TCGA-MN-A4N5 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MIA2 MUTATED                            1                                 3
  MIA2 WILD-TYPE                         17                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MIA2 MUTATED                                                    8
  MIA2 WILD-TYPE                                                287
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  MIA2 MUTATED                                            0
  MIA2 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  MIA2 MUTATED                                               0
  MIA2 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  MIA2 MUTATED                                0
  MIA2 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  MIA2 MUTATED                                    0
  MIA2 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  MIA2 MUTATED                              0                             1
  MIA2 WILD-TYPE                            2                            21
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  MIA2 MUTATED                                               0
  MIA2 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  MIA2 MUTATED                              0
  MIA2 WILD-TYPE                            9
D71V10, multiclass
                                                    clus
vv                                                   MIA2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   MIA2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
D71V12, continuous
                vv
clus              R0  R1  R2  RX
  MIA2 MUTATED     8   2   0   0
  MIA2 WILD-TYPE 302   9   4  25
D71V13, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  R0            8            302
  R1            2              9
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIA2 MUTATED                                  0     0
  MIA2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MIA2 MUTATED                           0    11
  MIA2 WILD-TYPE                        29   366
D71V14, multiclass
                                  clus
vv                                 MIA2 MUTATED MIA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                      11            366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V15, binary
                cls
clus               0   1
  MIA2 MUTATED     0   8
  MIA2 WILD-TYPE   6 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      0    8
  MIA2 WILD-TYPE    6  341
                        clus
vv                       MIA2 MUTATED MIA2 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            8            341
[1] 2 2
[1] FALSE

Clustering(72) Variable = TUBB4 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  TUBB4 MUTATED    14   2
  TUBB4 WILD-TYPE 288 153
  TUBB4 MUTATED TUBB4 WILD-TYPE 
             16             441 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              2             153 
$`TUBB4 MUTATED`
TCGA-05-4397 TCGA-44-8119 TCGA-53-7813 TCGA-55-6985 TCGA-55-7576 TCGA-55-A490 
       24.03         3.25        13.94        40.54         1.32         1.58 
TCGA-64-5778 TCGA-64-5781 TCGA-67-4679 TCGA-69-7980 TCGA-73-4662 TCGA-91-A4BC 
       42.90        51.25        14.73        12.56        82.68         1.45 
TCGA-97-8174 TCGA-L9-A444 TCGA-NJ-A4YP TCGA-NJ-A4YQ 
        5.39        10.09         1.64        29.13 

$`TUBB4 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       36.99         7.59        27.25        34.29        30.54        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       24.99       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
        7.99         0.20         0.13         3.12        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 
        2.17        16.93        22.65        20.71        21.40        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       19.59         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       39.25        40.96        29.92        56.81        20.65        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 
       38.37        87.98         2.04        28.41        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        4.41         2.93        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
        2.01         6.90        52.60        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
       14.27         1.18        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 
       35.47        32.48        19.00        14.30         6.35        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A55A 
       19.13        73.91        71.05        62.60         0.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  TUBB4 MUTATED TUBB4 WILD-TYPE 
           1.32            0.00 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
          82.68          238.29 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
          13.25           19.82 
[1] "1.3 - 82.7 (13.2)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "2.4"
D72V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TUBB4 MUTATED         1        3        5         3         2          1
  TUBB4 WILD-TYPE       3      120      127        44        64         69
                 vv
clus              STAGE IIIB STAGE IV
  TUBB4 MUTATED            1        0
  TUBB4 WILD-TYPE         10       25
D72V3, multiclass
            clus
vv           TUBB4 MUTATED TUBB4 WILD-TYPE
  STAGE I                1               3
  STAGE IA               3             120
  STAGE IB               5             127
  STAGE IIA              3              44
  STAGE IIB              2              64
  STAGE IIIA             1              69
  STAGE IIIB             1              10
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TUBB4 MUTATED     4  10   2   1
  TUBB4 WILD-TYPE 151 251  41  17
D72V4, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  T1             4             151
  T2            10             251
  T3             2              41
  T4             1              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
  TUBB4 MUTATED    15   1     1
  TUBB4 WILD-TYPE 292  88    71
D72V5, multiclass
       clus
vv      TUBB4 MUTATED TUBB4 WILD-TYPE
  N0               15             292
  N1                1              88
  N2+N3             1              71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                 cls
clus                0   1
  TUBB4 MUTATED    13   0
  TUBB4 WILD-TYPE 315  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED     13    0
  TUBB4 WILD-TYPE  315   23
   clus
vv  TUBB4 MUTATED TUBB4 WILD-TYPE
  0            13             315
  1             0              23
[1] 2 2
[1] FALSE
D72V7, binary
                 cls
clus                0   1
  TUBB4 MUTATED     8   9
  TUBB4 WILD-TYPE 251 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      8    9
  TUBB4 WILD-TYPE  251  212
        clus
vv       TUBB4 MUTATED TUBB4 WILD-TYPE
  FEMALE             8             251
  MALE               9             212
[1] 2 2
[1] FALSE
D72V8, binary
                 cls
clus                0   1
  TUBB4 MUTATED    10   0
  TUBB4 WILD-TYPE 323  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED     10    0
  TUBB4 WILD-TYPE  323   49
     clus
vv    TUBB4 MUTATED TUBB4 WILD-TYPE
  NO             10             323
  YES             0              49
[1] 2 2
[1] FALSE
D72V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TUBB4 MUTATED                            0                                 2
  TUBB4 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TUBB4 MUTATED                                                   11
  TUBB4 WILD-TYPE                                                284
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TUBB4 MUTATED                                            0
  TUBB4 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TUBB4 MUTATED                                               2
  TUBB4 WILD-TYPE                                            17
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  TUBB4 MUTATED                                0
  TUBB4 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  TUBB4 MUTATED                                    0
  TUBB4 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TUBB4 MUTATED                              0                             2
  TUBB4 WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TUBB4 MUTATED                                               0
  TUBB4 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  TUBB4 MUTATED                              0
  TUBB4 WILD-TYPE                            9
D72V10, multiclass
                                                    clus
vv                                                   TUBB4 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  2
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   TUBB4 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   17
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, continuous
D72V12, continuous
                 vv
clus               R0  R1  R2  RX
  TUBB4 MUTATED    10   0   0   1
  TUBB4 WILD-TYPE 300  11   4  24
D72V13, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  R0            10             300
  R1             0              11
  R2             0               4
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TUBB4 MUTATED                                  0     0
  TUBB4 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TUBB4 MUTATED                           1    14
  TUBB4 WILD-TYPE                        28   363
D72V14, multiclass
                                  clus
vv                                 TUBB4 MUTATED TUBB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       14             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, binary
                 cls
clus                0   1
  TUBB4 MUTATED     0  14
  TUBB4 WILD-TYPE   6 335
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      0   14
  TUBB4 WILD-TYPE    6  335
                        clus
vv                       TUBB4 MUTATED TUBB4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            14             335
[1] 2 2
[1] FALSE

Clustering(73) Variable = ABHD12B MUTATION ANALYSIS
D73V1, survival
                   sevent
clus2                 0   1
  ABHD12B MUTATED     3   4
  ABHD12B WILD-TYPE 299 151
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                7               450 
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                4               151 
$`ABHD12B MUTATED`
TCGA-44-6779 TCGA-49-4501 TCGA-55-6968 TCGA-55-7994 TCGA-78-7147 TCGA-99-8032 
       16.44        46.72        42.51        19.82        19.27         1.45 
TCGA-NJ-A4YP 
        1.64 

$`ABHD12B WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       32.45        61.28        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       12.66        35.54        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       50.33       163.10        27.16         5.69        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85        36.76        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13        29.13         0.26         0.43        19.82        59.11 

  ABHD12B MUTATED ABHD12B WILD-TYPE 
             1.45              0.00 
  ABHD12B MUTATED ABHD12B WILD-TYPE 
            46.72            238.29 
  ABHD12B MUTATED ABHD12B WILD-TYPE 
            19.27             19.82 
[1] "1.4 - 46.7 (19.3)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "2"  
D73V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ABHD12B MUTATED         0        1        2         0         3          0
  ABHD12B WILD-TYPE       4      122      130        47        63         70
                   vv
clus                STAGE IIIB STAGE IV
  ABHD12B MUTATED            0        1
  ABHD12B WILD-TYPE         11       24
D73V3, multiclass
            clus
vv           ABHD12B MUTATED ABHD12B WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 2               130
  STAGE IIA                0                47
  STAGE IIB                3                63
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ABHD12B MUTATED     2   4   1   0
  ABHD12B WILD-TYPE 153 257  42  18
D73V4, multiclass
    clus
vv   ABHD12B MUTATED ABHD12B WILD-TYPE
  T1               2               153
  T2               4               257
  T3               1                42
  T4               0                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
  ABHD12B MUTATED     5   2     0
  ABHD12B WILD-TYPE 302  87    72
D73V5, multiclass
       clus
vv      ABHD12B MUTATED ABHD12B WILD-TYPE
  N0                  5               302
  N1                  2                87
  N2+N3               0                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                   cls
clus                  0   1
  ABHD12B MUTATED     4   1
  ABHD12B WILD-TYPE 324  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      4    1
  ABHD12B WILD-TYPE  324   22
   clus
vv  ABHD12B MUTATED ABHD12B WILD-TYPE
  0               4               324
  1               1                22
[1] 2 2
[1] FALSE
D73V7, binary
                   cls
clus                  0   1
  ABHD12B MUTATED     3   4
  ABHD12B WILD-TYPE 256 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      3    4
  ABHD12B WILD-TYPE  256  217
        clus
vv       ABHD12B MUTATED ABHD12B WILD-TYPE
  FEMALE               3               256
  MALE                 4               217
[1] 2 2
[1] FALSE
D73V8, binary
                   cls
clus                  0   1
  ABHD12B MUTATED     6   1
  ABHD12B WILD-TYPE 327  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      6    1
  ABHD12B WILD-TYPE  327   48
     clus
vv    ABHD12B MUTATED ABHD12B WILD-TYPE
  NO                6               327
  YES               1                48
[1] 2 2
[1] FALSE
D73V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ABHD12B MUTATED                            0
  ABHD12B WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ABHD12B MUTATED                                   0
  ABHD12B WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ABHD12B MUTATED                                                    6
  ABHD12B WILD-TYPE                                                289
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ABHD12B MUTATED                                            0
  ABHD12B WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ABHD12B MUTATED                                               0
  ABHD12B WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  ABHD12B MUTATED                                0
  ABHD12B WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  ABHD12B MUTATED                                    0
  ABHD12B WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ABHD12B MUTATED                              0                             1
  ABHD12B WILD-TYPE                            2                            21
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ABHD12B MUTATED                                               0
  ABHD12B WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  ABHD12B MUTATED                              0
  ABHD12B WILD-TYPE                            9
D73V10, multiclass
                                                    clus
vv                                                   ABHD12B MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   ABHD12B WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, continuous
D73V12, continuous
                   vv
clus                 R0  R1  R2  RX
  ABHD12B MUTATED     4   0   0   0
  ABHD12B WILD-TYPE 306  11   4  25
D73V13, multiclass
    clus
vv   ABHD12B MUTATED ABHD12B WILD-TYPE
  R0               4               306
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABHD12B MUTATED                                  0     0
  ABHD12B WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ABHD12B MUTATED                           0     7
  ABHD12B WILD-TYPE                        29   370
D73V14, multiclass
                                  clus
vv                                 ABHD12B MUTATED ABHD12B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          7               370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, binary
                   cls
clus                  0   1
  ABHD12B MUTATED     0   5
  ABHD12B WILD-TYPE   6 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      0    5
  ABHD12B WILD-TYPE    6  344
                        clus
vv                       ABHD12B MUTATED ABHD12B WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5               344
[1] 2 2
[1] FALSE

Clustering(74) Variable = ANTXR1 MUTATION ANALYSIS
D74V1, survival
                  sevent
clus2                0   1
  ANTXR1 MUTATED    14   5
  ANTXR1 WILD-TYPE 288 150
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              19              438 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
               5              150 
$`ANTXR1 MUTATED`
TCGA-38-4626 TCGA-49-4487 TCGA-55-7574 TCGA-55-7903 TCGA-55-7907 TCGA-55-8092 
      120.79        28.11         3.12        18.64         0.53         5.06 
TCGA-55-A491 TCGA-62-A472 TCGA-64-5779 TCGA-67-4679 TCGA-67-6215 TCGA-73-4668 
       20.58        29.92        28.41        14.73         5.72        15.35 
TCGA-78-8662 TCGA-97-7941 TCGA-97-8174 TCGA-99-8028 TCGA-L4-A4E5 TCGA-L9-A443 
      110.50         0.72         5.39        36.76        19.00         6.35 
TCGA-L9-A444 
       10.09 

$`ANTXR1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        13.45        76.21        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 
        0.59         1.15         7.99         0.20         0.13         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        1.45         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
       29.72        15.19         3.29        19.66        19.73         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 
       16.93        22.65        20.71        21.40         1.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.04         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
        6.90        52.60        23.38        82.68        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8171 TCGA-97-8172 
       43.79        25.48         5.95         0.59        18.67        17.92 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 
       18.67        20.68        24.56        34.85         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       24.30        23.80        18.08        35.47        32.48        14.30 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
            0.53             0.00 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
          120.79           238.29 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
          15.350           19.855 
[1] "0.5 - 120.8 (15.3)" "0.0 - 238.3 (19.9)"
[1] "hr=" "1.3"
D74V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ANTXR1 MUTATED         1        7        3         3         3          1
  ANTXR1 WILD-TYPE       3      116      129        44        63         69
                  vv
clus               STAGE IIIB STAGE IV
  ANTXR1 MUTATED            0        0
  ANTXR1 WILD-TYPE         11       25
D74V3, multiclass
            clus
vv           ANTXR1 MUTATED ANTXR1 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                7              116
  STAGE IB                3              129
  STAGE IIA               3               44
  STAGE IIB               3               63
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANTXR1 MUTATED     8   8   3   0
  ANTXR1 WILD-TYPE 147 253  40  18
D74V4, multiclass
    clus
vv   ANTXR1 MUTATED ANTXR1 WILD-TYPE
  T1              8              147
  T2              8              253
  T3              3               40
  T4              0               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
  ANTXR1 MUTATED    16   2     1
  ANTXR1 WILD-TYPE 291  87    71
D74V5, multiclass
       clus
vv      ANTXR1 MUTATED ANTXR1 WILD-TYPE
  N0                16              291
  N1                 2               87
  N2+N3              1               71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED    12   0
  ANTXR1 WILD-TYPE 316  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED     12    0
  ANTXR1 WILD-TYPE  316   23
   clus
vv  ANTXR1 MUTATED ANTXR1 WILD-TYPE
  0             12              316
  1              0               23
[1] 2 2
[1] FALSE
D74V7, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED    12   7
  ANTXR1 WILD-TYPE 247 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED     12    7
  ANTXR1 WILD-TYPE  247  214
        clus
vv       ANTXR1 MUTATED ANTXR1 WILD-TYPE
  FEMALE             12              247
  MALE                7              214
[1] 2 2
[1] FALSE
D74V8, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED    13   2
  ANTXR1 WILD-TYPE 320  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED     13    2
  ANTXR1 WILD-TYPE  320   47
     clus
vv    ANTXR1 MUTATED ANTXR1 WILD-TYPE
  NO              13              320
  YES              2               47
[1] 2 2
[1] FALSE
D74V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ANTXR1 MUTATED                            2                                 0
  ANTXR1 WILD-TYPE                         16                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ANTXR1 MUTATED                                                   15
  ANTXR1 WILD-TYPE                                                280
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ANTXR1 MUTATED                                            0
  ANTXR1 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ANTXR1 MUTATED                                               0
  ANTXR1 WILD-TYPE                                            19
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ANTXR1 MUTATED                                0
  ANTXR1 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ANTXR1 MUTATED                                    1
  ANTXR1 WILD-TYPE                                  2
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ANTXR1 MUTATED                              0                             1
  ANTXR1 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ANTXR1 MUTATED                                               0
  ANTXR1 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ANTXR1 MUTATED                              0
  ANTXR1 WILD-TYPE                            9
D74V10, multiclass
                                                    clus
vv                                                   ANTXR1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   0
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              1
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ANTXR1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    19
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, continuous
D74V12, continuous
                  vv
clus                R0  R1  R2  RX
  ANTXR1 MUTATED    17   1   0   0
  ANTXR1 WILD-TYPE 293  10   4  25
D74V13, multiclass
    clus
vv   ANTXR1 MUTATED ANTXR1 WILD-TYPE
  R0             17              293
  R1              1               10
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANTXR1 MUTATED                                  1     0
  ANTXR1 WILD-TYPE                                0     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANTXR1 MUTATED                           1    16
  ANTXR1 WILD-TYPE                        28   361
D74V14, multiclass
                                  clus
vv                                 ANTXR1 MUTATED ANTXR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                        16              361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     0  18
  ANTXR1 WILD-TYPE   6 331
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      0   18
  ANTXR1 WILD-TYPE    6  331
                        clus
vv                       ANTXR1 MUTATED ANTXR1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             18              331
[1] 2 2
[1] FALSE

Clustering(75) Variable = FLCN MUTATION ANALYSIS
D75V1, survival
                sevent
clus2              0   1
  FLCN MUTATED     4   5
  FLCN WILD-TYPE 298 150
  FLCN MUTATED FLCN WILD-TYPE 
             9            448 
  FLCN MUTATED FLCN WILD-TYPE 
             5            150 
$`FLCN MUTATED`
TCGA-05-4397 TCGA-53-7626 TCGA-55-7281 TCGA-55-8511 TCGA-62-A46O TCGA-78-7154 
       24.03        30.54         0.59         0.30        47.80        19.50 
TCGA-78-7537 TCGA-93-A4JN TCGA-97-8175 
       53.33        23.61        18.12 

$`FLCN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
       10.13        36.99         7.59        27.25        34.29        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       49.25        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       51.25        28.47        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        6.90        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95       119.51        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53        31.20         8.02        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO 
        1.45        19.82        22.45        17.46         6.12         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29        41.82        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        5.39        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.26         0.43        19.82        59.11 

  FLCN MUTATED FLCN WILD-TYPE 
           0.3            0.0 
  FLCN MUTATED FLCN WILD-TYPE 
         53.33         238.29 
  FLCN MUTATED FLCN WILD-TYPE 
         23.61          19.79 
[1] "0.3 - 53.3 (23.6)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.7"
D75V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FLCN MUTATED         0        1        4         1         1          1
  FLCN WILD-TYPE       4      122      128        46        65         69
                vv
clus             STAGE IIIB STAGE IV
  FLCN MUTATED            0        1
  FLCN WILD-TYPE         11       24
D75V3, multiclass
            clus
vv           FLCN MUTATED FLCN WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              4            128
  STAGE IIA             1             46
  STAGE IIB             1             65
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FLCN MUTATED     2   6   1   0
  FLCN WILD-TYPE 153 255  42  18
D75V4, multiclass
    clus
vv   FLCN MUTATED FLCN WILD-TYPE
  T1            2            153
  T2            6            255
  T3            1             42
  T4            0             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
  FLCN MUTATED     6   2     1
  FLCN WILD-TYPE 301  87    71
D75V5, multiclass
       clus
vv      FLCN MUTATED FLCN WILD-TYPE
  N0               6            301
  N1               2             87
  N2+N3            1             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                cls
clus               0   1
  FLCN MUTATED     7   1
  FLCN WILD-TYPE 321  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      7    1
  FLCN WILD-TYPE  321   22
   clus
vv  FLCN MUTATED FLCN WILD-TYPE
  0            7            321
  1            1             22
[1] 2 2
[1] FALSE
D75V7, binary
                cls
clus               0   1
  FLCN MUTATED     5   4
  FLCN WILD-TYPE 254 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      5    4
  FLCN WILD-TYPE  254  217
        clus
vv       FLCN MUTATED FLCN WILD-TYPE
  FEMALE            5            254
  MALE              4            217
[1] 2 2
[1] FALSE
D75V8, binary
                cls
clus               0   1
  FLCN MUTATED     6   0
  FLCN WILD-TYPE 327  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      6    0
  FLCN WILD-TYPE  327   49
     clus
vv    FLCN MUTATED FLCN WILD-TYPE
  NO             6            327
  YES            0             49
[1] 2 2
[1] FALSE
D75V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FLCN MUTATED                            1                                 2
  FLCN WILD-TYPE                         17                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FLCN MUTATED                                                    5
  FLCN WILD-TYPE                                                290
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FLCN MUTATED                                            0
  FLCN WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FLCN MUTATED                                               0
  FLCN WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  FLCN MUTATED                                0
  FLCN WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  FLCN MUTATED                                    0
  FLCN WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FLCN MUTATED                              0                             0
  FLCN WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FLCN MUTATED                                               1
  FLCN WILD-TYPE                                             4
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  FLCN MUTATED                              0
  FLCN WILD-TYPE                            9
D75V10, multiclass
                                                    clus
vv                                                   FLCN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 1
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   FLCN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   4
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, continuous
D75V12, continuous
                vv
clus              R0  R1  R2  RX
  FLCN MUTATED     7   0   0   1
  FLCN WILD-TYPE 303  11   4  24
D75V13, multiclass
    clus
vv   FLCN MUTATED FLCN WILD-TYPE
  R0            7            303
  R1            0             11
  R2            0              4
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLCN MUTATED                                  0     0
  FLCN WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FLCN MUTATED                           0     7
  FLCN WILD-TYPE                        29   370
D75V14, multiclass
                                  clus
vv                                 FLCN MUTATED FLCN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             29
  WHITE                                       7            370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V15, binary
                cls
clus               0   1
  FLCN MUTATED     0   5
  FLCN WILD-TYPE   6 344
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      0    5
  FLCN WILD-TYPE    6  344
                        clus
vv                       FLCN MUTATED FLCN WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            344
[1] 2 2
[1] FALSE

Clustering(76) Variable = ZNF556 MUTATION ANALYSIS
D76V1, survival
                  sevent
clus2                0   1
  ZNF556 MUTATED     8   4
  ZNF556 WILD-TYPE 294 151
  ZNF556 MUTATED ZNF556 WILD-TYPE 
              12              445 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
               4              151 
$`ZNF556 MUTATED`
TCGA-05-4405 TCGA-05-4424 TCGA-38-4630 TCGA-50-5946 TCGA-55-6982 TCGA-55-7994 
       20.05        30.02        35.28        22.55        32.71        19.82 
TCGA-55-8301 TCGA-69-7979 TCGA-91-6829 TCGA-97-8179 TCGA-99-8028 TCGA-MP-A4TF 
        1.45         2.93        41.36        14.30        36.76        11.05 

$`ZNF556 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       25.12        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        7.79         2.20        45.34        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
      107.21        70.26         1.74         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
        1.28         1.12         0.79         1.78         1.45        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         4.41        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24        17.16         2.01         6.90        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        50.33       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        9.57       104.19       238.29         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
       24.23        13.64        26.47        10.62         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       18.12        15.39        16.41        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.68        24.56        34.85         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        6.35        10.09        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ZNF556 MUTATED ZNF556 WILD-TYPE 
            1.45             0.00 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
           41.36           238.29 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
           21.30            19.73 
[1] "1.4 - 41.4 (21.3)"  "0.0 - 238.3 (19.7)"
[1] "hr=" "1.2"
D76V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ZNF556 MUTATED         0        3        5         1         3          0
  ZNF556 WILD-TYPE       4      120      127        46        63         70
                  vv
clus               STAGE IIIB STAGE IV
  ZNF556 MUTATED            0        0
  ZNF556 WILD-TYPE         11       25
D76V3, multiclass
            clus
vv           ZNF556 MUTATED ZNF556 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              120
  STAGE IB                5              127
  STAGE IIA               1               46
  STAGE IIB               3               63
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF556 MUTATED     3   7   2   0
  ZNF556 WILD-TYPE 152 254  41  18
D76V4, multiclass
    clus
vv   ZNF556 MUTATED ZNF556 WILD-TYPE
  T1              3              152
  T2              7              254
  T3              2               41
  T4              0               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
  ZNF556 MUTATED    11   1     0
  ZNF556 WILD-TYPE 296  88    72
D76V5, multiclass
       clus
vv      ZNF556 MUTATED ZNF556 WILD-TYPE
  N0                11              296
  N1                 1               88
  N2+N3              0               72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     7   0
  ZNF556 WILD-TYPE 321  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      7    0
  ZNF556 WILD-TYPE  321   23
   clus
vv  ZNF556 MUTATED ZNF556 WILD-TYPE
  0              7              321
  1              0               23
[1] 2 2
[1] FALSE
D76V7, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     6   6
  ZNF556 WILD-TYPE 253 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      6    6
  ZNF556 WILD-TYPE  253  215
        clus
vv       ZNF556 MUTATED ZNF556 WILD-TYPE
  FEMALE              6              253
  MALE                6              215
[1] 2 2
[1] FALSE
D76V8, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     7   2
  ZNF556 WILD-TYPE 326  47
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      7    2
  ZNF556 WILD-TYPE  326   47
     clus
vv    ZNF556 MUTATED ZNF556 WILD-TYPE
  NO               7              326
  YES              2               47
[1] 2 2
[1] FALSE
D76V9, continuous
[1] "Remove cluster labels:" "ZNF556 MUTATED"        
clus
  ZNF556 MUTATED ZNF556 WILD-TYPE 
               1              116 
      TCGA-35-4122       TCGA-35-4123       TCGA-35-5375       TCGA-44-3396 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-44-3918       TCGA-44-4112       TCGA-44-6144       TCGA-44-6147 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-44-6775       TCGA-44-7660       TCGA-44-A47F       TCGA-49-4486 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-49-4494       TCGA-49-4505       TCGA-49-4506       TCGA-49-4510 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-49-6742       TCGA-49-6743       TCGA-49-6744       TCGA-53-7624 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-53-A4EZ       TCGA-55-7283       TCGA-55-7573       TCGA-55-7725 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-7910       TCGA-55-7914       TCGA-55-8089       TCGA-55-8096 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-8205       TCGA-55-8208       TCGA-55-8507       TCGA-55-8508 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-8511       TCGA-55-8512       TCGA-55-8619       TCGA-55-8620 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-8621       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A491 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-A492       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1677       TCGA-64-1681 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-64-5775       TCGA-64-5778       TCGA-69-7974       TCGA-69-8254 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-71-6725       TCGA-71-8520       TCGA-73-4659       TCGA-73-4662 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-73-4666       TCGA-73-4668       TCGA-73-4670       TCGA-73-4676 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-73-4677       TCGA-73-7498       TCGA-73-7499       TCGA-75-5122 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-6562       TCGA-86-6851       TCGA-86-7701 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-7711       TCGA-86-7713       TCGA-86-7714       TCGA-86-7953 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8054       TCGA-86-8055 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8073       TCGA-86-8074       TCGA-86-8075 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-8076       TCGA-86-8278       TCGA-86-8279       TCGA-86-8280 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-8281       TCGA-86-8358       TCGA-86-8359       TCGA-86-8668 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-8669       TCGA-86-8671       TCGA-86-A456       TCGA-86-A4JF 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-A4P7       TCGA-91-6849       TCGA-93-7347       TCGA-93-7348 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-93-8067       TCGA-93-A4JN       TCGA-93-A4JO       TCGA-95-7567 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-99-7458       TCGA-MN-A4N1       TCGA-MN-A4N4       TCGA-MN-A4N5 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF556 MUTATED                            2                                 3
  ZNF556 WILD-TYPE                         16                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF556 MUTATED                                                    5
  ZNF556 WILD-TYPE                                                290
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ZNF556 MUTATED                                            0
  ZNF556 WILD-TYPE                                          4
                  vv
clus               LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ZNF556 MUTATED                                               1
  ZNF556 WILD-TYPE                                            18
                  vv
clus               LUNG CLEAR CELL ADENOCARCINOMA
  ZNF556 MUTATED                                0
  ZNF556 WILD-TYPE                              2
                  vv
clus               LUNG MICROPAPILLARY ADENOCARCINOMA
  ZNF556 MUTATED                                    0
  ZNF556 WILD-TYPE                                  3
                  vv
clus               LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ZNF556 MUTATED                              0                             1
  ZNF556 WILD-TYPE                            2                            21
                  vv
clus               LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ZNF556 MUTATED                                               0
  ZNF556 WILD-TYPE                                             5
                  vv
clus               MUCINOUS (COLLOID) CARCINOMA
  ZNF556 MUTATED                              0
  ZNF556 WILD-TYPE                            9
D76V10, multiclass
                                                    clus
vv                                                   ZNF556 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   1
  LUNG CLEAR CELL ADENOCARCINOMA                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   0
  MUCINOUS (COLLOID) CARCINOMA                                    0
                                                    clus
vv                                                   ZNF556 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                       16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    18
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      2
  LUNG PAPILLARY ADENOCARCINOMA                                    21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     5
  MUCINOUS (COLLOID) CARCINOMA                                      9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, continuous
D76V12, continuous
                  vv
clus                R0  R1  R2  RX
  ZNF556 MUTATED     6   2   0   0
  ZNF556 WILD-TYPE 304   9   4  25
D76V13, multiclass
    clus
vv   ZNF556 MUTATED ZNF556 WILD-TYPE
  R0              6              304
  R1              2                9
  R2              0                4
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF556 MUTATED                                  0     0
  ZNF556 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF556 MUTATED                           1     9
  ZNF556 WILD-TYPE                        28   368
D76V14, multiclass
                                  clus
vv                                 ZNF556 MUTATED ZNF556 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               28
  WHITE                                         9              368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V15, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     0   8
  ZNF556 WILD-TYPE   6 341
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      0    8
  ZNF556 WILD-TYPE    6  341
                        clus
vv                       ZNF556 MUTATED ZNF556 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              8              341
[1] 2 2
[1] FALSE

Clustering(77) Variable = ASCL3 MUTATION ANALYSIS
D77V1, survival
                 sevent
clus2               0   1
  ASCL3 MUTATED     4   3
  ASCL3 WILD-TYPE 298 152
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              7             450 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              3             152 
$`ASCL3 MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-50-5939 TCGA-55-8094 TCGA-55-A4DG TCGA-86-A4JF 
       19.96         8.02        15.12         0.13        19.99        24.23 
TCGA-95-7039 
       41.82 

$`ASCL3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03        47.05        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 
       40.60        78.67        21.47         8.45         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       51.25        28.47        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        6.90        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       28.34        26.50        29.46        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ASCL3 MUTATED ASCL3 WILD-TYPE 
           0.13            0.00 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
          41.82          238.29 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
          19.96           19.79 
[1] "0.1 - 41.8 (20.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.8"
D77V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ASCL3 MUTATED         0        1        2         0         2          0
  ASCL3 WILD-TYPE       4      122      130        47        64         70
                 vv
clus              STAGE IIIB STAGE IV
  ASCL3 MUTATED            0        2
  ASCL3 WILD-TYPE         11       23
D77V3, multiclass
            clus
vv           ASCL3 MUTATED ASCL3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             122
  STAGE IB               2             130
  STAGE IIA              0              47
  STAGE IIB              2              64
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               2              23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASCL3 MUTATED     1   4   2   0
  ASCL3 WILD-TYPE 154 257  41  18
D77V4, multiclass
    clus
vv   ASCL3 MUTATED ASCL3 WILD-TYPE
  T1             1             154
  T2             4             257
  T3             2              41
  T4             0              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
  ASCL3 MUTATED     6   0     0
  ASCL3 WILD-TYPE 301  89    72
D77V5, multiclass
       clus
vv      ASCL3 MUTATED ASCL3 WILD-TYPE
  N0                6             301
  N1                0              89
  N2+N3             0              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                 cls
clus                0   1
  ASCL3 MUTATED     3   2
  ASCL3 WILD-TYPE 325  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      3    2
  ASCL3 WILD-TYPE  325   21
   clus
vv  ASCL3 MUTATED ASCL3 WILD-TYPE
  0             3             325
  1             2              21
[1] 2 2
[1] FALSE
D77V7, binary
                 cls
clus                0   1
  ASCL3 MUTATED     2   5
  ASCL3 WILD-TYPE 257 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      2    5
  ASCL3 WILD-TYPE  257  216
        clus
vv       ASCL3 MUTATED ASCL3 WILD-TYPE
  FEMALE             2             257
  MALE               5             216
[1] 2 2
[1] FALSE
D77V8, binary
                 cls
clus                0   1
  ASCL3 MUTATED     5   0
  ASCL3 WILD-TYPE 328  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      5    0
  ASCL3 WILD-TYPE  328   49
     clus
vv    ASCL3 MUTATED ASCL3 WILD-TYPE
  NO              5             328
  YES             0              49
[1] 2 2
[1] FALSE
D77V9, continuous
[1] "Remove cluster labels:" "ASCL3 MUTATED"         
clus
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              1             116 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-44-3396 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-6144      TCGA-44-6147 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-44-A47F      TCGA-49-4486 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-49-4494      TCGA-49-4505      TCGA-49-4506      TCGA-49-4510 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-49-6742      TCGA-49-6743      TCGA-49-6744      TCGA-53-7624 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-7283      TCGA-55-7573      TCGA-55-7725 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7914      TCGA-55-8089      TCGA-55-8096 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8208      TCGA-55-8507      TCGA-55-8508 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8511      TCGA-55-8512      TCGA-55-8619      TCGA-55-8620 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8621      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-69-7974      TCGA-69-8254 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4659      TCGA-73-4662 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-73-4666      TCGA-73-4668      TCGA-73-4670      TCGA-73-4676 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-73-4677      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-6562      TCGA-86-6851      TCGA-86-7701 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7713      TCGA-86-7714      TCGA-86-7953 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8054      TCGA-86-8055 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8075 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8280 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8281      TCGA-86-8358      TCGA-86-8359      TCGA-86-8668 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8669      TCGA-86-8671      TCGA-86-A456      TCGA-86-A4P7 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-91-6829      TCGA-91-6849      TCGA-93-7347      TCGA-93-7348 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-99-7458      TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ASCL3 MUTATED                            0                                 3
  ASCL3 WILD-TYPE                         18                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ASCL3 MUTATED                                                    4
  ASCL3 WILD-TYPE                                                291
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ASCL3 MUTATED                                            0
  ASCL3 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ASCL3 MUTATED                                               0
  ASCL3 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ASCL3 MUTATED                                0
  ASCL3 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ASCL3 MUTATED                                    0
  ASCL3 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ASCL3 MUTATED                              0                             0
  ASCL3 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ASCL3 MUTATED                                               0
  ASCL3 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ASCL3 MUTATED                              0
  ASCL3 WILD-TYPE                            9
D77V10, multiclass
                                                    clus
vv                                                   ASCL3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ASCL3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, continuous
D77V12, continuous
[1] "Remove cluster labels:" "ASCL3 MUTATED"         
clus
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              1             256 
     TCGA-05-4384      TCGA-05-4390      TCGA-05-4396      TCGA-05-4405 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4415      TCGA-05-4417      TCGA-05-4424 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-4433      TCGA-05-5420      TCGA-05-5423 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-05-5425      TCGA-05-5428      TCGA-35-4122      TCGA-35-4123 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-35-5375      TCGA-38-4625      TCGA-38-4626      TCGA-38-7271 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-38-A44F      TCGA-44-2656      TCGA-44-2657      TCGA-44-3396 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-3398      TCGA-44-3918      TCGA-44-4112      TCGA-44-5644 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-5645      TCGA-44-6144      TCGA-44-6145      TCGA-44-6147 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-6148      TCGA-44-6774      TCGA-44-6775      TCGA-44-6776 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-6777      TCGA-44-6778      TCGA-44-6779      TCGA-44-7659 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-7660      TCGA-44-7661      TCGA-44-7662      TCGA-44-7667 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7670      TCGA-44-7672      TCGA-44-8117 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-8119      TCGA-44-8120      TCGA-44-A479      TCGA-44-A47A 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-A47B      TCGA-44-A47F      TCGA-44-A47G      TCGA-44-A4SS 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4494      TCGA-49-4505 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-1592      TCGA-55-1595      TCGA-55-5899      TCGA-55-6642 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-6712      TCGA-55-6971      TCGA-55-7227      TCGA-55-7283 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7570      TCGA-55-7574      TCGA-55-7576      TCGA-55-7724 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7728      TCGA-55-7907 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7911      TCGA-55-7914      TCGA-55-8089 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8092      TCGA-55-8096      TCGA-55-8097      TCGA-55-8205 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8299      TCGA-55-8301      TCGA-55-8302      TCGA-55-8506 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8511      TCGA-55-8512      TCGA-55-8514 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8615      TCGA-55-8620      TCGA-55-8621      TCGA-55-A48X 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A493      TCGA-55-A494      TCGA-62-8398 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-64-1677      TCGA-64-1681      TCGA-64-5774      TCGA-64-5775 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-64-5778      TCGA-64-5779      TCGA-64-5781      TCGA-69-7761 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-69-7763      TCGA-69-7764      TCGA-69-7765      TCGA-69-7974 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-69-7979      TCGA-69-8253      TCGA-69-8255      TCGA-69-A59K 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4662      TCGA-73-4666      TCGA-73-4668 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-73-4670      TCGA-73-4675      TCGA-73-4676      TCGA-73-7498 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-75-6214      TCGA-75-7025      TCGA-75-7027      TCGA-75-7031 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7145      TCGA-78-7146      TCGA-78-7147      TCGA-78-7148 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7149      TCGA-78-7150      TCGA-78-7152      TCGA-78-7153 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7154      TCGA-78-7155      TCGA-78-7156      TCGA-78-7158 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7159      TCGA-78-7160      TCGA-78-7161      TCGA-78-7162 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7163      TCGA-78-7166      TCGA-78-7167      TCGA-78-7220 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7535      TCGA-78-7536      TCGA-78-7537      TCGA-78-7539 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7542      TCGA-78-7633      TCGA-78-8640      TCGA-78-8648 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8660      TCGA-78-8662      TCGA-80-5607 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-80-5608      TCGA-83-5908      TCGA-86-6851      TCGA-86-7711 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7954      TCGA-86-8054      TCGA-86-8055 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8281 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8669      TCGA-86-8673 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8674      TCGA-86-A456      TCGA-91-6829      TCGA-91-6830 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-91-6836      TCGA-91-6840      TCGA-91-6849      TCGA-91-8499 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-91-A4BC      TCGA-93-7347      TCGA-93-7348      TCGA-93-8067 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-93-A4JQ      TCGA-95-7043 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-95-7562      TCGA-95-7567      TCGA-95-7944      TCGA-95-7947 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN      TCGA-95-A4VP 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-7546      TCGA-97-7553      TCGA-97-7554      TCGA-97-7941 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-8171      TCGA-97-8172      TCGA-97-8174      TCGA-97-8176 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-8179      TCGA-97-A4LX      TCGA-97-A4M0      TCGA-97-A4M1 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M5      TCGA-97-A4M7 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-99-7458      TCGA-99-8025      TCGA-99-8028      TCGA-99-8032 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-J2-8194      TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-L4-A4E6      TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MN-A4N4      TCGA-MN-A4N5      TCGA-MP-A4SV      TCGA-MP-A4SW 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A4T2      TCGA-MP-A4T4      TCGA-MP-A4T7      TCGA-MP-A4T8 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A4T9      TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TE 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A5C7      TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  ASCL3 MUTATED     4   0   1   0
  ASCL3 WILD-TYPE 306  11   3  25
D77V13, multiclass
    clus
vv   ASCL3 MUTATED ASCL3 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             1               3
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASCL3 MUTATED                                  0     0
  ASCL3 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASCL3 MUTATED                           0     5
  ASCL3 WILD-TYPE                        29   372
D77V14, multiclass
                                  clus
vv                                 ASCL3 MUTATED ASCL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        5             372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V15, binary
                 cls
clus                0   1
  ASCL3 MUTATED     0   5
  ASCL3 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      0    5
  ASCL3 WILD-TYPE    6  344
                        clus
vv                       ASCL3 MUTATED ASCL3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             344
[1] 2 2
[1] FALSE

Clustering(78) Variable = DSG3 MUTATION ANALYSIS
D78V1, survival
                sevent
clus2              0   1
  DSG3 MUTATED    19  14
  DSG3 WILD-TYPE 283 141
  DSG3 MUTATED DSG3 WILD-TYPE 
            33            424 
  DSG3 MUTATED DSG3 WILD-TYPE 
            14            141 
$`DSG3 MUTATED`
TCGA-05-4382 TCGA-05-4430 TCGA-05-5425 TCGA-44-2656 TCGA-44-6777 TCGA-44-7669 
       19.96        25.02        29.00        46.98        32.45        18.87 
TCGA-44-A47G TCGA-50-5930 TCGA-50-5932 TCGA-50-5936 TCGA-50-6590 TCGA-50-6594 
       11.54         9.27        40.60         8.45        42.35        12.16 
TCGA-53-7626 TCGA-55-1592 TCGA-55-6981 TCGA-55-7911 TCGA-55-7994 TCGA-55-8085 
       30.54        23.05        45.34        17.65        19.82        29.72 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 TCGA-55-A490 TCGA-69-7974 TCGA-69-A59K 
        0.36         0.49         0.30         1.58         6.05        17.16 
TCGA-73-4670 TCGA-78-7161 TCGA-86-A4JF TCGA-91-6829 TCGA-95-7948 TCGA-97-A4M0 
        4.31         9.57        24.23        41.36        15.65        21.44 
TCGA-99-8032 TCGA-NJ-A4YI TCGA-NJ-A55A 
        1.45         0.13         0.26 

$`DSG3 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
       15.02         4.96        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        4.37        44.42        38.10        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        63.72        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
       12.03         7.17        36.07        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.08        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       15.72        60.16        31.04        49.28         8.09        14.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67        21.47        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 
       22.55         3.91        25.55        11.05         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99         7.59        27.25        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94        35.21        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 
        3.88         5.49         7.79         2.20        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 
        1.45        18.64         0.53         6.48         6.15         0.16 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.95         0.26 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       21.40        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         5.42         7.56         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 
       12.56        14.01        13.45         4.24         2.01         6.90 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 
       52.60        23.38        82.68        26.30        15.35        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
       22.92       104.19       238.29         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        10.62         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        20.19        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       34.85        36.76        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP 
       14.10        19.13        73.91        71.05        62.60         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       29.13         0.43        19.82        59.11 

  DSG3 MUTATED DSG3 WILD-TYPE 
          0.13           0.00 
  DSG3 MUTATED DSG3 WILD-TYPE 
         46.98         238.29 
  DSG3 MUTATED DSG3 WILD-TYPE 
        17.650         19.855 
[1] "0.1 - 47.0 (17.6)"  "0.0 - 238.3 (19.9)"
[1] "hr=" "1.8"
D78V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DSG3 MUTATED         0        5       10         4         7          6
  DSG3 WILD-TYPE       4      118      122        43        59         64
                vv
clus             STAGE IIIB STAGE IV
  DSG3 MUTATED            0        1
  DSG3 WILD-TYPE         11       24
D78V3, multiclass
            clus
vv           DSG3 MUTATED DSG3 WILD-TYPE
  STAGE I               0              4
  STAGE IA              5            118
  STAGE IB             10            122
  STAGE IIA             4             43
  STAGE IIB             7             59
  STAGE IIIA            6             64
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSG3 MUTATED     7  20   6   0
  DSG3 WILD-TYPE 148 241  37  18
D78V4, multiclass
    clus
vv   DSG3 MUTATED DSG3 WILD-TYPE
  T1            7            148
  T2           20            241
  T3            6             37
  T4            0             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
  DSG3 MUTATED    21   5     6
  DSG3 WILD-TYPE 286  84    66
D78V5, multiclass
       clus
vv      DSG3 MUTATED DSG3 WILD-TYPE
  N0              21            286
  N1               5             84
  N2+N3            6             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                cls
clus               0   1
  DSG3 MUTATED    22   1
  DSG3 WILD-TYPE 306  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     22    1
  DSG3 WILD-TYPE  306   22
   clus
vv  DSG3 MUTATED DSG3 WILD-TYPE
  0           22            306
  1            1             22
[1] 2 2
[1] FALSE
D78V7, binary
                cls
clus               0   1
  DSG3 MUTATED    19  14
  DSG3 WILD-TYPE 240 207
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     19   14
  DSG3 WILD-TYPE  240  207
        clus
vv       DSG3 MUTATED DSG3 WILD-TYPE
  FEMALE           19            240
  MALE             14            207
[1] 2 2
[1] FALSE
D78V8, binary
                cls
clus               0   1
  DSG3 MUTATED    23   4
  DSG3 WILD-TYPE 310  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     23    4
  DSG3 WILD-TYPE  310   45
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  NO            23            310
  YES            4             45
[1] 2 2
[1] FALSE
D78V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DSG3 MUTATED                            0                                 9
  DSG3 WILD-TYPE                         18                                92
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DSG3 MUTATED                                                   19
  DSG3 WILD-TYPE                                                276
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DSG3 MUTATED                                            0
  DSG3 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DSG3 MUTATED                                               1
  DSG3 WILD-TYPE                                            18
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  DSG3 MUTATED                                0
  DSG3 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  DSG3 MUTATED                                    0
  DSG3 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DSG3 MUTATED                              0                             2
  DSG3 WILD-TYPE                            2                            20
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DSG3 MUTATED                                               0
  DSG3 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  DSG3 MUTATED                              2
  DSG3 WILD-TYPE                            7
D78V10, multiclass
                                                    clus
vv                                                   DSG3 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           19
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 1
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  2
                                                    clus
vv                                                   DSG3 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            276
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V11, continuous
D78V12, continuous
                vv
clus              R0  R1  R2  RX
  DSG3 MUTATED    19   1   0   0
  DSG3 WILD-TYPE 291  10   4  25
D78V13, multiclass
    clus
vv   DSG3 MUTATED DSG3 WILD-TYPE
  R0           19            291
  R1            1             10
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSG3 MUTATED                                  0     0
  DSG3 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSG3 MUTATED                           4    26
  DSG3 WILD-TYPE                        25   351
D78V14, multiclass
                                  clus
vv                                 DSG3 MUTATED DSG3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   4             25
  WHITE                                      26            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V15, binary
                cls
clus               0   1
  DSG3 MUTATED     0  27
  DSG3 WILD-TYPE   6 322
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED      0   27
  DSG3 WILD-TYPE    6  322
                        clus
vv                       DSG3 MUTATED DSG3 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           27            322
[1] 2 2
[1] FALSE

Clustering(79) Variable = C5AR1 MUTATION ANALYSIS
D79V1, survival
                 sevent
clus2               0   1
  C5AR1 MUTATED     4   1
  C5AR1 WILD-TYPE 298 154
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              5             452 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              1             154 
$`C5AR1 MUTATED`
TCGA-05-4427 TCGA-05-5420 TCGA-73-4658 TCGA-86-8358 TCGA-97-7937 
       26.01        15.02        52.60        21.47         5.95 

$`C5AR1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 
        4.24        17.16         2.01         6.90        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       31.69        64.60        63.52        43.79        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        6.35        10.09        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  C5AR1 MUTATED C5AR1 WILD-TYPE 
           5.95            0.00 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
          52.60          238.29 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
          21.47           19.79 
[1] "6.0 - 52.6 (21.5)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.7"
D79V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C5AR1 MUTATED         0        0        3         0         1          1
  C5AR1 WILD-TYPE       4      123      129        47        65         69
                 vv
clus              STAGE IIIB STAGE IV
  C5AR1 MUTATED            0        0
  C5AR1 WILD-TYPE         11       25
D79V3, multiclass
            clus
vv           C5AR1 MUTATED C5AR1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             123
  STAGE IB               3             129
  STAGE IIA              0              47
  STAGE IIB              1              65
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  C5AR1 MUTATED     0   5   0   0
  C5AR1 WILD-TYPE 155 256  43  18
D79V4, multiclass
    clus
vv   C5AR1 MUTATED C5AR1 WILD-TYPE
  T1             0             155
  T2             5             256
  T3             0              43
  T4             0              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
  C5AR1 MUTATED     3   1     1
  C5AR1 WILD-TYPE 304  88    71
D79V5, multiclass
       clus
vv      C5AR1 MUTATED C5AR1 WILD-TYPE
  N0                3             304
  N1                1              88
  N2+N3             1              71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                 cls
clus                0   1
  C5AR1 MUTATED     4   0
  C5AR1 WILD-TYPE 324  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      4    0
  C5AR1 WILD-TYPE  324   23
   clus
vv  C5AR1 MUTATED C5AR1 WILD-TYPE
  0             4             324
  1             0              23
[1] 2 2
[1] FALSE
D79V7, binary
                 cls
clus                0   1
  C5AR1 MUTATED     2   3
  C5AR1 WILD-TYPE 257 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      2    3
  C5AR1 WILD-TYPE  257  218
        clus
vv       C5AR1 MUTATED C5AR1 WILD-TYPE
  FEMALE             2             257
  MALE               3             218
[1] 2 2
[1] FALSE
D79V8, binary
                 cls
clus                0   1
  C5AR1 MUTATED     3   0
  C5AR1 WILD-TYPE 330  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      3    0
  C5AR1 WILD-TYPE  330   49
     clus
vv    C5AR1 MUTATED C5AR1 WILD-TYPE
  NO              3             330
  YES             0              49
[1] 2 2
[1] FALSE
D79V9, continuous
[1] "Remove cluster labels:" "C5AR1 MUTATED"         
clus
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              1             116 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-44-3396 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-6144      TCGA-44-6147 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-44-A47F      TCGA-49-4486 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-49-4494      TCGA-49-4505      TCGA-49-4506      TCGA-49-4510 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-49-6742      TCGA-49-6743      TCGA-49-6744      TCGA-53-7624 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-7283      TCGA-55-7573      TCGA-55-7725 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7914      TCGA-55-8089      TCGA-55-8096 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-8205      TCGA-55-8208      TCGA-55-8507      TCGA-55-8508 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-8511      TCGA-55-8512      TCGA-55-8619      TCGA-55-8620 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-8621      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A491 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-A492      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1677      TCGA-64-1681 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-69-7974      TCGA-69-8254 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4659      TCGA-73-4662 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-73-4666      TCGA-73-4668      TCGA-73-4670      TCGA-73-4676 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-73-4677      TCGA-73-7498      TCGA-73-7499      TCGA-75-5122 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-6562      TCGA-86-6851      TCGA-86-7701 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-7711      TCGA-86-7713      TCGA-86-7714      TCGA-86-7953 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-7955      TCGA-86-8054      TCGA-86-8055 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8056      TCGA-86-8073      TCGA-86-8074      TCGA-86-8075 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8076      TCGA-86-8278      TCGA-86-8279      TCGA-86-8280 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8281      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-91-6829      TCGA-91-6849      TCGA-93-7347      TCGA-93-7348 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-93-8067      TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-99-7458      TCGA-MN-A4N1      TCGA-MN-A4N4      TCGA-MN-A4N5 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  C5AR1 MUTATED                            0                                 1
  C5AR1 WILD-TYPE                         18                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C5AR1 MUTATED                                                    3
  C5AR1 WILD-TYPE                                                292
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  C5AR1 MUTATED                                            0
  C5AR1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  C5AR1 MUTATED                                               0
  C5AR1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  C5AR1 MUTATED                                0
  C5AR1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  C5AR1 MUTATED                                    1
  C5AR1 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  C5AR1 MUTATED                              0                             0
  C5AR1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  C5AR1 MUTATED                                               0
  C5AR1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  C5AR1 MUTATED                              0
  C5AR1 WILD-TYPE                            9
D79V10, multiclass
                                                    clus
vv                                                   C5AR1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   C5AR1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V11, continuous
D79V12, continuous
                 vv
clus               R0  R1  R2  RX
  C5AR1 MUTATED     4   0   0   0
  C5AR1 WILD-TYPE 306  11   4  25
D79V13, multiclass
    clus
vv   C5AR1 MUTATED C5AR1 WILD-TYPE
  R0             4             306
  R1             0              11
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C5AR1 MUTATED                                  0     0
  C5AR1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  C5AR1 MUTATED                           0     3
  C5AR1 WILD-TYPE                        29   374
D79V14, multiclass
                                  clus
vv                                 C5AR1 MUTATED C5AR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                        3             374
[1] 4 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
  C5AR1 MUTATED     0   3
  C5AR1 WILD-TYPE   6 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      0    3
  C5AR1 WILD-TYPE    6  346
                        clus
vv                       C5AR1 MUTATED C5AR1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3             346
[1] 2 2
[1] FALSE

Clustering(80) Variable = ASXL2 MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2               0   1
  ASXL2 MUTATED    14   4
  ASXL2 WILD-TYPE 288 151
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             18             439 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              4             151 
$`ASXL2 MUTATED`
TCGA-05-4396 TCGA-05-4430 TCGA-44-3398 TCGA-44-8119 TCGA-55-6972 TCGA-55-6984 
        9.96        25.02        38.24         3.25        48.49        24.99 
TCGA-55-7574 TCGA-55-8302 TCGA-55-8620 TCGA-55-A493 TCGA-64-5781 TCGA-71-8520 
        3.12         0.76         2.17         0.92        51.25         6.90 
TCGA-78-8640 TCGA-86-8054 TCGA-86-A4JF TCGA-91-6831 TCGA-95-7947 TCGA-NJ-A4YP 
      232.18        37.74        24.23        10.19        15.68         1.64 

$`ASXL2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        46.98        44.42        38.10        42.77 
TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       29.00        29.23        13.74        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        2.20        45.34        32.71        60.03        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       70.26         1.74         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        0.13         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.58         1.61        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF 
       21.40         1.58        20.58        19.59        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       28.41        28.47        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        82.68        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        10.55        50.24        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       38.04        20.55        32.78        19.89        35.24         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
       13.64        26.47        10.62        41.36         1.97         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 
       41.82        16.54         2.86        18.67        12.39        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        6.35        10.09        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ASXL2 MUTATED ASXL2 WILD-TYPE 
           0.76            0.00 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         232.18          238.29 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         12.935          19.820 
[1] "0.8 - 232.2 (12.9)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.6"
D80V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ASXL2 MUTATED         0        2        9         1         4          0
  ASXL2 WILD-TYPE       4      121      123        46        62         70
                 vv
clus              STAGE IIIB STAGE IV
  ASXL2 MUTATED            1        1
  ASXL2 WILD-TYPE         10       24
D80V3, multiclass
            clus
vv           ASXL2 MUTATED ASXL2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             121
  STAGE IB               9             123
  STAGE IIA              1              46
  STAGE IIB              4              62
  STAGE IIIA             0              70
  STAGE IIIB             1              10
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASXL2 MUTATED     4  11   2   1
  ASXL2 WILD-TYPE 151 250  41  17
D80V4, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  T1             4             151
  T2            11             250
  T3             2              41
  T4             1              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
  ASXL2 MUTATED    13   5     0
  ASXL2 WILD-TYPE 294  84    72
D80V5, multiclass
       clus
vv      ASXL2 MUTATED ASXL2 WILD-TYPE
  N0               13             294
  N1                5              84
  N2+N3             0              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                 cls
clus                0   1
  ASXL2 MUTATED    15   1
  ASXL2 WILD-TYPE 313  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED     15    1
  ASXL2 WILD-TYPE  313   22
   clus
vv  ASXL2 MUTATED ASXL2 WILD-TYPE
  0            15             313
  1             1              22
[1] 2 2
[1] FALSE
D80V7, binary
                 cls
clus                0   1
  ASXL2 MUTATED     7  11
  ASXL2 WILD-TYPE 252 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      7   11
  ASXL2 WILD-TYPE  252  210
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  FEMALE             7             252
  MALE              11             210
[1] 2 2
[1] FALSE
D80V8, binary
                 cls
clus                0   1
  ASXL2 MUTATED    10   2
  ASXL2 WILD-TYPE 323  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED     10    2
  ASXL2 WILD-TYPE  323   47
     clus
vv    ASXL2 MUTATED ASXL2 WILD-TYPE
  NO             10             323
  YES             2              47
[1] 2 2
[1] FALSE
D80V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ASXL2 MUTATED                            1                                 4
  ASXL2 WILD-TYPE                         17                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ASXL2 MUTATED                                                   11
  ASXL2 WILD-TYPE                                                284
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ASXL2 MUTATED                                            0
  ASXL2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ASXL2 MUTATED                                               0
  ASXL2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ASXL2 MUTATED                                0
  ASXL2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ASXL2 MUTATED                                    0
  ASXL2 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ASXL2 MUTATED                              0                             2
  ASXL2 WILD-TYPE                            2                            20
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ASXL2 MUTATED                                               0
  ASXL2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ASXL2 MUTATED                              0
  ASXL2 WILD-TYPE                            9
D80V10, multiclass
                                                    clus
vv                                                   ASXL2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ASXL2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, continuous
D80V12, continuous
                 vv
clus               R0  R1  R2  RX
  ASXL2 MUTATED    13   1   0   0
  ASXL2 WILD-TYPE 297  10   4  25
D80V13, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  R0            13             297
  R1             1              10
  R2             0               4
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASXL2 MUTATED                                  0     1
  ASXL2 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASXL2 MUTATED                           0    14
  ASXL2 WILD-TYPE                        29   363
D80V14, multiclass
                                  clus
vv                                 ASXL2 MUTATED ASXL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              29
  WHITE                                       14             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V15, binary
                 cls
clus                0   1
  ASXL2 MUTATED     0  14
  ASXL2 WILD-TYPE   6 335
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      0   14
  ASXL2 WILD-TYPE    6  335
                        clus
vv                       ASXL2 MUTATED ASXL2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            14             335
[1] 2 2
[1] FALSE

Clustering(81) Variable = DLX5 MUTATION ANALYSIS
D81V1, survival
                sevent
clus2              0   1
  DLX5 MUTATED     7   6
  DLX5 WILD-TYPE 295 149
  DLX5 MUTATED DLX5 WILD-TYPE 
            13            444 
  DLX5 MUTATED DLX5 WILD-TYPE 
             6            149 
$`DLX5 MUTATED`
TCGA-38-4625 TCGA-50-6593 TCGA-55-8089 TCGA-55-8299 TCGA-55-8514 TCGA-86-6851 
       97.74        11.05         3.29        15.42         6.64         5.88 
TCGA-86-8054 TCGA-91-6828 TCGA-95-7043 TCGA-J2-A4AD TCGA-MP-A4T9 TCGA-MP-A4TA 
       37.74        10.62        16.54        18.08        41.59        31.23 
TCGA-NJ-A4YQ 
       29.13 

$`DLX5 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
        9.04         2.04         7.40         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51         2.17        22.16         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        0.10         4.80        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       51.25        28.47        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        6.90        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        4.31        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       77.59        10.55       110.50        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
       29.46        24.23        13.64        26.47        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29        41.82         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.57        24.30        23.80        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
        5.49         5.29         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.26         0.43        19.82        59.11 

  DLX5 MUTATED DLX5 WILD-TYPE 
          3.29           0.00 
  DLX5 MUTATED DLX5 WILD-TYPE 
         97.74         238.29 
  DLX5 MUTATED DLX5 WILD-TYPE 
         16.54          19.82 
[1] "3.3 - 97.7 (16.5)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.4"
D81V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DLX5 MUTATED         0        7        2         1         1          2
  DLX5 WILD-TYPE       4      116      130        46        65         68
                vv
clus             STAGE IIIB STAGE IV
  DLX5 MUTATED            0        0
  DLX5 WILD-TYPE         11       25
D81V3, multiclass
            clus
vv           DLX5 MUTATED DLX5 WILD-TYPE
  STAGE I               0              4
  STAGE IA              7            116
  STAGE IB              2            130
  STAGE IIA             1             46
  STAGE IIB             1             65
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DLX5 MUTATED     9   4   0   0
  DLX5 WILD-TYPE 146 257  43  18
D81V4, multiclass
    clus
vv   DLX5 MUTATED DLX5 WILD-TYPE
  T1            9            146
  T2            4            257
  T3            0             43
  T4            0             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
  DLX5 MUTATED     9   2     2
  DLX5 WILD-TYPE 298  87    70
D81V5, multiclass
       clus
vv      DLX5 MUTATED DLX5 WILD-TYPE
  N0               9            298
  N1               2             87
  N2+N3            2             70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                cls
clus               0   1
  DLX5 MUTATED     8   0
  DLX5 WILD-TYPE 320  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED      8    0
  DLX5 WILD-TYPE  320   23
   clus
vv  DLX5 MUTATED DLX5 WILD-TYPE
  0            8            320
  1            0             23
[1] 2 2
[1] FALSE
D81V7, binary
                cls
clus               0   1
  DLX5 MUTATED    10   3
  DLX5 WILD-TYPE 249 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED     10    3
  DLX5 WILD-TYPE  249  218
        clus
vv       DLX5 MUTATED DLX5 WILD-TYPE
  FEMALE           10            249
  MALE              3            218
[1] 2 2
[1] FALSE
D81V8, binary
                cls
clus               0   1
  DLX5 MUTATED    10   2
  DLX5 WILD-TYPE 323  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED     10    2
  DLX5 WILD-TYPE  323   47
     clus
vv    DLX5 MUTATED DLX5 WILD-TYPE
  NO            10            323
  YES            2             47
[1] 2 2
[1] FALSE
D81V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DLX5 MUTATED                            1                                 3
  DLX5 WILD-TYPE                         17                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DLX5 MUTATED                                                    9
  DLX5 WILD-TYPE                                                286
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DLX5 MUTATED                                            0
  DLX5 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DLX5 MUTATED                                               0
  DLX5 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  DLX5 MUTATED                                0
  DLX5 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  DLX5 MUTATED                                    0
  DLX5 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  DLX5 MUTATED                              0                             0
  DLX5 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DLX5 MUTATED                                               0
  DLX5 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  DLX5 MUTATED                              0
  DLX5 WILD-TYPE                            9
D81V10, multiclass
                                                    clus
vv                                                   DLX5 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   DLX5 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V11, continuous
D81V12, continuous
                vv
clus              R0  R1  R2  RX
  DLX5 MUTATED     8   0   0   3
  DLX5 WILD-TYPE 302  11   4  22
D81V13, multiclass
    clus
vv   DLX5 MUTATED DLX5 WILD-TYPE
  R0            8            302
  R1            0             11
  R2            0              4
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLX5 MUTATED                                  0     0
  DLX5 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DLX5 MUTATED                           1    12
  DLX5 WILD-TYPE                        28   365
D81V14, multiclass
                                  clus
vv                                 DLX5 MUTATED DLX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      12            365
[1] 4 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
  DLX5 MUTATED     0  13
  DLX5 WILD-TYPE   6 336
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED      0   13
  DLX5 WILD-TYPE    6  336
                        clus
vv                       DLX5 MUTATED DLX5 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           13            336
[1] 2 2
[1] FALSE

Clustering(82) Variable = ATAD2 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2               0   1
  ATAD2 MUTATED    10   3
  ATAD2 WILD-TYPE 292 152
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             13             444 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
              3             152 
$`ATAD2 MUTATED`
TCGA-05-4397 TCGA-44-5644 TCGA-44-6144 TCGA-55-7994 TCGA-64-1679 TCGA-64-5775 
       24.03        28.37        23.77        19.82        81.80         2.04 
TCGA-69-7979 TCGA-69-7980 TCGA-78-7633 TCGA-95-7567 TCGA-97-7937 TCGA-99-8025 
        2.93        12.56        50.24        18.67         5.95        34.85 
TCGA-MN-A4N4 
       38.63 

$`ATAD2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       33.30        28.01        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       20.65        38.37        87.98        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 
        5.42         7.56         6.05         4.41        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 
        4.24        17.16         2.01         6.90        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        50.33       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        9.57       104.19       238.29         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
       17.29        41.82        16.54         2.86        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       31.69        64.60        63.52        43.79        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       10.09        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        19.82        59.11 

  ATAD2 MUTATED ATAD2 WILD-TYPE 
           2.04            0.00 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
          81.80          238.29 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
         23.770          19.745 
[1] "2.0 - 81.8 (23.8)"  "0.0 - 238.3 (19.7)"
[1] "hr=" "1.6"
D82V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ATAD2 MUTATED         1        3        4         0         3          3
  ATAD2 WILD-TYPE       3      120      128        47        63         67
                 vv
clus              STAGE IIIB STAGE IV
  ATAD2 MUTATED            0        0
  ATAD2 WILD-TYPE         11       25
D82V3, multiclass
            clus
vv           ATAD2 MUTATED ATAD2 WILD-TYPE
  STAGE I                1               3
  STAGE IA               3             120
  STAGE IB               4             128
  STAGE IIA              0              47
  STAGE IIB              3              63
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATAD2 MUTATED     5   6   2   1
  ATAD2 WILD-TYPE 150 255  41  17
D82V4, multiclass
    clus
vv   ATAD2 MUTATED ATAD2 WILD-TYPE
  T1             5             150
  T2             6             255
  T3             2              41
  T4             1              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
  ATAD2 MUTATED     9   2     2
  ATAD2 WILD-TYPE 298  87    70
D82V5, multiclass
       clus
vv      ATAD2 MUTATED ATAD2 WILD-TYPE
  N0                9             298
  N1                2              87
  N2+N3             2              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                 cls
clus                0   1
  ATAD2 MUTATED    10   0
  ATAD2 WILD-TYPE 318  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED     10    0
  ATAD2 WILD-TYPE  318   23
   clus
vv  ATAD2 MUTATED ATAD2 WILD-TYPE
  0            10             318
  1             0              23
[1] 2 2
[1] FALSE
D82V7, binary
                 cls
clus                0   1
  ATAD2 MUTATED     5   9
  ATAD2 WILD-TYPE 254 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED      5    9
  ATAD2 WILD-TYPE  254  212
        clus
vv       ATAD2 MUTATED ATAD2 WILD-TYPE
  FEMALE             5             254
  MALE               9             212
[1] 2 2
[1] FALSE
D82V8, binary
                 cls
clus                0   1
  ATAD2 MUTATED     8   0
  ATAD2 WILD-TYPE 325  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED      8    0
  ATAD2 WILD-TYPE  325   49
     clus
vv    ATAD2 MUTATED ATAD2 WILD-TYPE
  NO              8             325
  YES             0              49
[1] 2 2
[1] FALSE
D82V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ATAD2 MUTATED                            1                                 3
  ATAD2 WILD-TYPE                         17                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ATAD2 MUTATED                                                    9
  ATAD2 WILD-TYPE                                                286
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ATAD2 MUTATED                                            0
  ATAD2 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ATAD2 MUTATED                                               0
  ATAD2 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  ATAD2 MUTATED                                0
  ATAD2 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  ATAD2 MUTATED                                    1
  ATAD2 WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ATAD2 MUTATED                              0                             0
  ATAD2 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ATAD2 MUTATED                                               0
  ATAD2 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  ATAD2 MUTATED                              0
  ATAD2 WILD-TYPE                            9
D82V10, multiclass
                                                    clus
vv                                                   ATAD2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             9
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   ATAD2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             286
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V11, continuous
D82V12, continuous
                 vv
clus               R0  R1  R2  RX
  ATAD2 MUTATED     7   0   0   1
  ATAD2 WILD-TYPE 303  11   4  24
D82V13, multiclass
    clus
vv   ATAD2 MUTATED ATAD2 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATAD2 MUTATED                                  0     0
  ATAD2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATAD2 MUTATED                           1    12
  ATAD2 WILD-TYPE                        28   365
D82V14, multiclass
                                  clus
vv                                 ATAD2 MUTATED ATAD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                       12             365
[1] 4 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
  ATAD2 MUTATED     0  12
  ATAD2 WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED      0   12
  ATAD2 WILD-TYPE    6  337
                        clus
vv                       ATAD2 MUTATED ATAD2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             337
[1] 2 2
[1] FALSE

Clustering(83) Variable = RAF1 MUTATION ANALYSIS
D83V1, survival
                sevent
clus2              0   1
  RAF1 MUTATED     5   1
  RAF1 WILD-TYPE 297 154
  RAF1 MUTATED RAF1 WILD-TYPE 
             6            451 
  RAF1 MUTATED RAF1 WILD-TYPE 
             1            154 
$`RAF1 MUTATED`
TCGA-05-4427 TCGA-55-8505 TCGA-69-7765 TCGA-78-7220 TCGA-97-7546 TCGA-J2-8192 
       26.01         0.95         5.42        26.53        31.69        24.30 

$`RAF1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       17.16        11.64        22.26        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94        35.21        23.05        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1.74         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        0.79         1.78         1.45        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.76         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
        6.64         6.12        22.68        13.61         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29         8.48        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
       24.56        34.85        36.76         1.45        21.57        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  RAF1 MUTATED RAF1 WILD-TYPE 
          0.95           0.00 
  RAF1 MUTATED RAF1 WILD-TYPE 
         31.69         238.29 
  RAF1 MUTATED RAF1 WILD-TYPE 
        25.155         19.760 
[1] "0.9 - 31.7 (25.2)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.4"
D83V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RAF1 MUTATED         0        1        0         1         1          2
  RAF1 WILD-TYPE       4      122      132        46        65         68
                vv
clus             STAGE IIIB STAGE IV
  RAF1 MUTATED            0        1
  RAF1 WILD-TYPE         11       24
D83V3, multiclass
            clus
vv           RAF1 MUTATED RAF1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            122
  STAGE IB              0            132
  STAGE IIA             1             46
  STAGE IIB             1             65
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RAF1 MUTATED     2   3   0   1
  RAF1 WILD-TYPE 153 258  43  17
D83V4, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  T1            2            153
  T2            3            258
  T3            0             43
  T4            1             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
  RAF1 MUTATED     2   2     2
  RAF1 WILD-TYPE 305  87    70
D83V5, multiclass
       clus
vv      RAF1 MUTATED RAF1 WILD-TYPE
  N0               2            305
  N1               2             87
  N2+N3            2             70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V6, binary
                cls
clus               0   1
  RAF1 MUTATED     2   0
  RAF1 WILD-TYPE 326  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      2    0
  RAF1 WILD-TYPE  326   23
   clus
vv  RAF1 MUTATED RAF1 WILD-TYPE
  0            2            326
  1            0             23
[1] 2 2
[1] FALSE
D83V7, binary
                cls
clus               0   1
  RAF1 MUTATED     4   2
  RAF1 WILD-TYPE 255 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      4    2
  RAF1 WILD-TYPE  255  219
        clus
vv       RAF1 MUTATED RAF1 WILD-TYPE
  FEMALE            4            255
  MALE              2            219
[1] 2 2
[1] FALSE
D83V8, binary
                cls
clus               0   1
  RAF1 MUTATED     3   1
  RAF1 WILD-TYPE 330  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      3    1
  RAF1 WILD-TYPE  330   48
     clus
vv    RAF1 MUTATED RAF1 WILD-TYPE
  NO             3            330
  YES            1             48
[1] 2 2
[1] FALSE
D83V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RAF1 MUTATED                            1                                 3
  RAF1 WILD-TYPE                         17                                98
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RAF1 MUTATED                                                    2
  RAF1 WILD-TYPE                                                293
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  RAF1 MUTATED                                            0
  RAF1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  RAF1 MUTATED                                               0
  RAF1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  RAF1 MUTATED                                0
  RAF1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  RAF1 MUTATED                                    0
  RAF1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  RAF1 MUTATED                              0                             0
  RAF1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  RAF1 MUTATED                                               0
  RAF1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  RAF1 MUTATED                              0
  RAF1 WILD-TYPE                            9
D83V10, multiclass
                                                    clus
vv                                                   RAF1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   RAF1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V11, continuous
D83V12, continuous
                vv
clus              R0  R1  R2  RX
  RAF1 MUTATED     4   0   0   0
  RAF1 WILD-TYPE 306  11   4  25
D83V13, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  R0            4            306
  R1            0             11
  R2            0              4
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAF1 MUTATED                                  0     0
  RAF1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAF1 MUTATED                           1     4
  RAF1 WILD-TYPE                        28   373
D83V14, multiclass
                                  clus
vv                                 RAF1 MUTATED RAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                       4            373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V15, binary
                cls
clus               0   1
  RAF1 MUTATED     0   4
  RAF1 WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      0    4
  RAF1 WILD-TYPE    6  345
                        clus
vv                       RAF1 MUTATED RAF1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            345
[1] 2 2
[1] FALSE

Clustering(84) Variable = A2M MUTATION ANALYSIS
D84V1, survival
               sevent
clus2             0   1
  A2M MUTATED    15   3
  A2M WILD-TYPE 287 152
  A2M MUTATED A2M WILD-TYPE 
           18           439 
  A2M MUTATED A2M WILD-TYPE 
            3           152 
$`A2M MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-38-4632 TCGA-55-1595 TCGA-55-8089 TCGA-55-8203 
        8.02        20.05        44.61        48.62         3.29        17.98 
TCGA-55-A490 TCGA-64-1676 TCGA-64-5781 TCGA-69-7980 TCGA-73-4670 TCGA-78-8640 
        1.58        56.81        51.25        12.56         4.31       232.18 
TCGA-86-8054 TCGA-91-6828 TCGA-91-6848 TCGA-95-7043 TCGA-97-7554 TCGA-MN-A4N4 
       37.74        10.62         7.36        16.54        25.48        38.63 

$`A2M WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
        0.00         9.96        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        11.64        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
        4.37        46.98        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       23.05         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        0.13        23.64        15.65         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.41        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        4.41         2.93        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35        30.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55        50.24        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
       29.46        24.23        13.64        26.47        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
       10.19         2.60        13.71        12.23        27.68         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29        41.82         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       31.69        64.60        63.52        43.79         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       24.56        34.85        36.76         1.45        21.57        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        6.35        10.09        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  A2M MUTATED A2M WILD-TYPE 
         1.58          0.00 
  A2M MUTATED A2M WILD-TYPE 
       232.18        238.29 
  A2M MUTATED A2M WILD-TYPE 
       19.015        19.820 
[1] "1.6 - 232.2 (19.0)" "0.0 - 238.3 (19.8)"
[1] "hr=" "2.7"
D84V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  A2M MUTATED         1        7        3         2         2          2
  A2M WILD-TYPE       3      116      129        45        64         68
               vv
clus            STAGE IIIB STAGE IV
  A2M MUTATED            0        3
  A2M WILD-TYPE         11       22
D84V3, multiclass
            clus
vv           A2M MUTATED A2M WILD-TYPE
  STAGE I              1             3
  STAGE IA             7           116
  STAGE IB             3           129
  STAGE IIA            2            45
  STAGE IIB            2            64
  STAGE IIIA           2            68
  STAGE IIIB           0            11
  STAGE IV             3            22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  A2M MUTATED     9  10   1   0
  A2M WILD-TYPE 146 251  42  18
D84V4, multiclass
    clus
vv   A2M MUTATED A2M WILD-TYPE
  T1           9           146
  T2          10           251
  T3           1            42
  T4           0            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
  A2M MUTATED    14   3     2
  A2M WILD-TYPE 293  86    70
D84V5, multiclass
       clus
vv      A2M MUTATED A2M WILD-TYPE
  N0             14           293
  N1              3            86
  N2+N3           2            70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V6, binary
               cls
clus              0   1
  A2M MUTATED    14   3
  A2M WILD-TYPE 314  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED     14    3
  A2M WILD-TYPE  314   20
   clus
vv  A2M MUTATED A2M WILD-TYPE
  0          14           314
  1           3            20
[1] 2 2
[1] FALSE
D84V7, binary
               cls
clus              0   1
  A2M MUTATED    10  10
  A2M WILD-TYPE 249 211
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED     10   10
  A2M WILD-TYPE  249  211
        clus
vv       A2M MUTATED A2M WILD-TYPE
  FEMALE          10           249
  MALE            10           211
[1] 2 2
[1] FALSE
D84V8, binary
               cls
clus              0   1
  A2M MUTATED    16   0
  A2M WILD-TYPE 317  49
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED     16    0
  A2M WILD-TYPE  317   49
     clus
vv    A2M MUTATED A2M WILD-TYPE
  NO           16           317
  YES           0            49
[1] 2 2
[1] FALSE
D84V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  A2M MUTATED                            1                                 4
  A2M WILD-TYPE                         17                                97
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  A2M MUTATED                                                   13
  A2M WILD-TYPE                                                282
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  A2M MUTATED                                            0
  A2M WILD-TYPE                                          4
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  A2M MUTATED                                               0
  A2M WILD-TYPE                                            19
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  A2M MUTATED                                1
  A2M WILD-TYPE                              1
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  A2M MUTATED                                    0                            0
  A2M WILD-TYPE                                  3                            2
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  A2M MUTATED                               1
  A2M WILD-TYPE                            21
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  A2M MUTATED                                               0
  A2M WILD-TYPE                                             5
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  A2M MUTATED                              0
  A2M WILD-TYPE                            9
D84V10, multiclass
                                                    clus
vv                                                   A2M MUTATED A2M WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                   1            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          13           282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                0            19
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                                1            21
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                0             5
  MUCINOUS (COLLOID) CARCINOMA                                 0             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V11, continuous
D84V12, continuous
               vv
clus             R0  R1  R2  RX
  A2M MUTATED    15   0   1   0
  A2M WILD-TYPE 295  11   3  25
D84V13, multiclass
    clus
vv   A2M MUTATED A2M WILD-TYPE
  R0          15           295
  R1           0            11
  R2           1             3
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  A2M MUTATED                                  0     1
  A2M WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  A2M MUTATED                           1    13
  A2M WILD-TYPE                        28   364
D84V14, multiclass
                                  clus
vv                                 A2M MUTATED A2M WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  1            28
  WHITE                                     13           364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V15, binary
               cls
clus              0   1
  A2M MUTATED     0  15
  A2M WILD-TYPE   6 334
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED      0   15
  A2M WILD-TYPE    6  334
                        clus
vv                       A2M MUTATED A2M WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          15           334
[1] 2 2
[1] FALSE

Clustering(85) Variable = SND1 MUTATION ANALYSIS
D85V1, survival
                sevent
clus2              0   1
  SND1 MUTATED     9   7
  SND1 WILD-TYPE 293 148
  SND1 MUTATED SND1 WILD-TYPE 
            16            441 
  SND1 MUTATED SND1 WILD-TYPE 
             7            148 
$`SND1 MUTATED`
TCGA-05-4415 TCGA-44-3918 TCGA-50-5930 TCGA-50-6594 TCGA-64-1676 TCGA-69-7978 
        2.99        34.06         9.27        12.16        56.81         4.41 
TCGA-78-7155 TCGA-78-7166 TCGA-86-7701 TCGA-86-7955 TCGA-86-8358 TCGA-86-8359 
       38.50         8.48        31.13        35.24        21.47        14.60 
TCGA-91-6828 TCGA-95-7043 TCGA-95-7947 TCGA-NJ-A4YQ 
       10.62        16.54        15.68        29.13 

$`SND1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       42.77        37.15        38.24        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         8.09        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26         1.74         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
        1.28         1.28         1.12         0.79         1.78         1.45 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.10         4.80         6.64        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
       72.30        13.61        39.25        40.96        29.92        20.65 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       51.25        28.47        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 
       13.61         5.42         7.56         6.05         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        17.16         2.01         6.90 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        82.68        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.95       119.51        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09        12.36         5.88        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       32.78        19.89        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       26.50        29.46        24.23        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29        41.82         2.86        18.67 
TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
       19.00        14.30         6.35        10.09        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       73.91        71.05        62.60         0.13         1.64         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  SND1 MUTATED SND1 WILD-TYPE 
          2.99           0.00 
  SND1 MUTATED SND1 WILD-TYPE 
         56.81         238.29 
  SND1 MUTATED SND1 WILD-TYPE 
         16.11          19.82 
[1] "3.0 - 56.8 (16.1)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.6"
D85V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SND1 MUTATED         0        6        3         0         2          3
  SND1 WILD-TYPE       4      117      129        47        64         67
                vv
clus             STAGE IIIB STAGE IV
  SND1 MUTATED            1        1
  SND1 WILD-TYPE         10       24
D85V3, multiclass
            clus
vv           SND1 MUTATED SND1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              6            117
  STAGE IB              3            129
  STAGE IIA             0             47
  STAGE IIB             2             64
  STAGE IIIA            3             67
  STAGE IIIB            1             10
  STAGE IV              1             24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SND1 MUTATED     6   7   2   1
  SND1 WILD-TYPE 149 254  41  17
D85V4, multiclass
    clus
vv   SND1 MUTATED SND1 WILD-TYPE
  T1            6            149
  T2            7            254
  T3            2             41
  T4            1             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
  SND1 MUTATED    10   2     4
  SND1 WILD-TYPE 297  87    68
D85V5, multiclass
       clus
vv      SND1 MUTATED SND1 WILD-TYPE
  N0              10            297
  N1               2             87
  N2+N3            4             68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V6, binary
                cls
clus               0   1
  SND1 MUTATED    13   1
  SND1 WILD-TYPE 315  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED     13    1
  SND1 WILD-TYPE  315   22
   clus
vv  SND1 MUTATED SND1 WILD-TYPE
  0           13            315
  1            1             22
[1] 2 2
[1] FALSE
D85V7, binary
                cls
clus               0   1
  SND1 MUTATED     4  12
  SND1 WILD-TYPE 255 209
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED      4   12
  SND1 WILD-TYPE  255  209
        clus
vv       SND1 MUTATED SND1 WILD-TYPE
  FEMALE            4            255
  MALE             12            209
[1] 2 2
[1] FALSE
D85V8, binary
                cls
clus               0   1
  SND1 MUTATED    10   3
  SND1 WILD-TYPE 323  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED     10    3
  SND1 WILD-TYPE  323   46
     clus
vv    SND1 MUTATED SND1 WILD-TYPE
  NO            10            323
  YES            3             46
[1] 2 2
[1] FALSE
D85V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SND1 MUTATED                            0                                 5
  SND1 WILD-TYPE                         18                                96
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SND1 MUTATED                                                   11
  SND1 WILD-TYPE                                                284
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  SND1 MUTATED                                            0
  SND1 WILD-TYPE                                          4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  SND1 MUTATED                                               0
  SND1 WILD-TYPE                                            19
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  SND1 MUTATED                                0
  SND1 WILD-TYPE                              2
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  SND1 MUTATED                                    0
  SND1 WILD-TYPE                                  3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  SND1 MUTATED                              0                             0
  SND1 WILD-TYPE                            2                            22
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  SND1 MUTATED                                               0
  SND1 WILD-TYPE                                             5
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  SND1 MUTATED                              0
  SND1 WILD-TYPE                            9
D85V10, multiclass
                                                    clus
vv                                                   SND1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                    0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                 0
  LUNG CLEAR CELL ADENOCARCINOMA                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                            0
  LUNG MUCINOUS ADENOCARCINOMA                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                 0
  MUCINOUS (COLLOID) CARCINOMA                                  0
                                                    clus
vv                                                   SND1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                     18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  19
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   5
  MUCINOUS (COLLOID) CARCINOMA                                    9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V11, continuous
D85V12, continuous
                vv
clus              R0  R1  R2  RX
  SND1 MUTATED    10   0   0   2
  SND1 WILD-TYPE 300  11   4  23
D85V13, multiclass
    clus
vv   SND1 MUTATED SND1 WILD-TYPE
  R0           10            300
  R1            0             11
  R2            0              4
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SND1 MUTATED                                  0     0
  SND1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SND1 MUTATED                           1    14
  SND1 WILD-TYPE                        28   363
D85V14, multiclass
                                  clus
vv                                 SND1 MUTATED SND1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             28
  WHITE                                      14            363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V15, binary
                cls
clus               0   1
  SND1 MUTATED     0  13
  SND1 WILD-TYPE   6 336
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED      0   13
  SND1 WILD-TYPE    6  336
                        clus
vv                       SND1 MUTATED SND1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           13            336
[1] 2 2
[1] FALSE

Clustering(86) Variable = C7ORF36 MUTATION ANALYSIS
D86V1, survival
                   sevent
clus2                 0   1
  C7ORF36 MUTATED     3   3
  C7ORF36 WILD-TYPE 299 152
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
                6               451 
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
                3               152 
$`C7ORF36 MUTATED`
TCGA-05-4382 TCGA-49-4486 TCGA-55-8506 TCGA-73-4658 TCGA-78-7149 TCGA-78-7536 
       19.96        76.21         0.36        52.60       129.53         8.02 

$`C7ORF36 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        13.45        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
       17.16         2.01         6.90        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       50.33       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        26.53        31.20        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       26.50        29.46        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       10.09        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
             0.36              0.00 
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
           129.53            238.29 
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
            36.28             19.76 
[1] "0.4 - 129.5 (36.3)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.4"
D86V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C7ORF36 MUTATED         0        1        2         0         1          1
  C7ORF36 WILD-TYPE       4      122      130        47        65         69
                   vv
clus                STAGE IIIB STAGE IV
  C7ORF36 MUTATED            1        0
  C7ORF36 WILD-TYPE         10       25
D86V3, multiclass
            clus
vv           C7ORF36 MUTATED C7ORF36 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               122
  STAGE IB                 2               130
  STAGE IIA                0                47
  STAGE IIB                1                65
  STAGE IIIA               1                69
  STAGE IIIB               1                10
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF36 MUTATED     1   3   1   1
  C7ORF36 WILD-TYPE 154 258  42  17
D86V4, multiclass
    clus
vv   C7ORF36 MUTATED C7ORF36 WILD-TYPE
  T1               1               154
  T2               3               258
  T3               1                42
  T4               1                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
  C7ORF36 MUTATED     5   0     1
  C7ORF36 WILD-TYPE 302  89    71
D86V5, multiclass
       clus
vv      C7ORF36 MUTATED C7ORF36 WILD-TYPE
  N0                  5               302
  N1                  0                89
  N2+N3               1                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V6, binary
                   cls
clus                  0   1
  C7ORF36 MUTATED     5   0
  C7ORF36 WILD-TYPE 323  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF36 MUTATED      5    0
  C7ORF36 WILD-TYPE  323   23
   clus
vv  C7ORF36 MUTATED C7ORF36 WILD-TYPE
  0               5               323
  1               0                23
[1] 2 2
[1] FALSE
D86V7, binary
                   cls
clus                  0   1
  C7ORF36 MUTATED     2   4
  C7ORF36 WILD-TYPE 257 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF36 MUTATED      2    4
  C7ORF36 WILD-TYPE  257  217
        clus
vv       C7ORF36 MUTATED C7ORF36 WILD-TYPE
  FEMALE               2               257
  MALE                 4               217
[1] 2 2
[1] FALSE
D86V8, binary
                   cls
clus                  0   1
  C7ORF36 MUTATED     3   1
  C7ORF36 WILD-TYPE 330  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF36 MUTATED      3    1
  C7ORF36 WILD-TYPE  330   48
     clus
vv    C7ORF36 MUTATED C7ORF36 WILD-TYPE
  NO                3               330
  YES               1                48
[1] 2 2
[1] FALSE
D86V9, continuous
[1] "Remove cluster labels:" "C7ORF36 MUTATED"       
clus
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
                1               116 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-44-3396 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-44-3918        TCGA-44-4112        TCGA-44-6144        TCGA-44-6147 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-44-6775        TCGA-44-7660        TCGA-44-A47F        TCGA-49-4494 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-49-4505        TCGA-49-4506        TCGA-49-4510        TCGA-49-6742 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-49-6743        TCGA-49-6744        TCGA-53-7624        TCGA-53-A4EZ 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7573        TCGA-55-7725        TCGA-55-7910 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-7914        TCGA-55-8089        TCGA-55-8096        TCGA-55-8205 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-8208        TCGA-55-8507        TCGA-55-8508        TCGA-55-8511 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8619        TCGA-55-8620        TCGA-55-8621 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-A48Z        TCGA-55-A490        TCGA-55-A491        TCGA-55-A492 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-A494        TCGA-62-8394        TCGA-62-8395        TCGA-62-8397 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-62-8398        TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-62-A46P        TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-62-A46V        TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-62-A472        TCGA-64-1677        TCGA-64-1681        TCGA-64-5775 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-64-5778        TCGA-69-7974        TCGA-69-8254        TCGA-71-6725 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-71-8520        TCGA-73-4659        TCGA-73-4662        TCGA-73-4666 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-73-4668        TCGA-73-4670        TCGA-73-4676        TCGA-73-4677 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-73-7498        TCGA-73-7499        TCGA-75-5122        TCGA-83-5908 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-6562        TCGA-86-6851        TCGA-86-7701        TCGA-86-7711 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7953        TCGA-86-7954 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-7955        TCGA-86-8054        TCGA-86-8055        TCGA-86-8056 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-8073        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8280        TCGA-86-8281 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8359        TCGA-86-8668        TCGA-86-8669 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-8671        TCGA-86-A456        TCGA-86-A4JF        TCGA-86-A4P7 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-91-6829        TCGA-91-6849        TCGA-93-7347        TCGA-93-7348 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-93-8067        TCGA-93-A4JN        TCGA-93-A4JO        TCGA-95-7567 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-99-7458        TCGA-MN-A4N1        TCGA-MN-A4N4        TCGA-MN-A4N5 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  C7ORF36 MUTATED                            0
  C7ORF36 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  C7ORF36 MUTATED                                   2
  C7ORF36 WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C7ORF36 MUTATED                                                    4
  C7ORF36 WILD-TYPE                                                291
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  C7ORF36 MUTATED                                            0
  C7ORF36 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  C7ORF36 MUTATED                                               0
  C7ORF36 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  C7ORF36 MUTATED                                0
  C7ORF36 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  C7ORF36 MUTATED                                    0
  C7ORF36 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  C7ORF36 MUTATED                              0                             0
  C7ORF36 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  C7ORF36 MUTATED                                               0
  C7ORF36 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  C7ORF36 MUTATED                              0
  C7ORF36 WILD-TYPE                            9
D86V10, multiclass
                                                    clus
vv                                                   C7ORF36 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   C7ORF36 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V11, continuous
D86V12, continuous
                   vv
clus                 R0  R1  R2  RX
  C7ORF36 MUTATED     6   0   0   0
  C7ORF36 WILD-TYPE 304  11   4  25
D86V13, multiclass
    clus
vv   C7ORF36 MUTATED C7ORF36 WILD-TYPE
  R0               6               304
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF36 MUTATED                                  0     0
  C7ORF36 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C7ORF36 MUTATED                           0     5
  C7ORF36 WILD-TYPE                        29   372
D86V14, multiclass
                                  clus
vv                                 C7ORF36 MUTATED C7ORF36 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          5               372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V15, binary
                   cls
clus                  0   1
  C7ORF36 MUTATED     0   3
  C7ORF36 WILD-TYPE   6 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF36 MUTATED      0    3
  C7ORF36 WILD-TYPE    6  346
                        clus
vv                       C7ORF36 MUTATED C7ORF36 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               3               346
[1] 2 2
[1] FALSE

Clustering(87) Variable = HTRA1 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2               0   1
  HTRA1 MUTATED     6   3
  HTRA1 WILD-TYPE 296 152
  HTRA1 MUTATED HTRA1 WILD-TYPE 
              9             448 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
              3             152 
$`HTRA1 MUTATED`
TCGA-05-5425 TCGA-49-6745 TCGA-55-8507 TCGA-78-7156 TCGA-86-8055 TCGA-99-8025 
       29.00        17.16         0.26        32.09         4.08        34.85 
TCGA-MN-A4N4 TCGA-NJ-A4YQ TCGA-O1-A52J 
       38.63        29.13        59.11 

$`HTRA1 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02        15.02         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       14.73        26.30         4.37        46.98        44.42        38.10 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       60.03        24.99        40.54       107.21        70.26         1.74 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.78         1.45        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.36         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41         2.93        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        35.24        37.74         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       16.54         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        36.76         1.45        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       10.09        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        1.64         0.26         0.43        19.82 

  HTRA1 MUTATED HTRA1 WILD-TYPE 
           0.26            0.00 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
          59.11          238.29 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
         29.130          19.745 
[1] "0.3 - 59.1 (29.1)"  "0.0 - 238.3 (19.7)"
[1] "hr=" "1.2"
D87V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  HTRA1 MUTATED         0        4        1         1         1          2
  HTRA1 WILD-TYPE       4      119      131        46        65         68
                 vv
clus              STAGE IIIB STAGE IV
  HTRA1 MUTATED            0        1
  HTRA1 WILD-TYPE         11       24
D87V3, multiclass
            clus
vv           HTRA1 MUTATED HTRA1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             119
  STAGE IB               1             131
  STAGE IIA              1              46
  STAGE IIB              1              65
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              24
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HTRA1 MUTATED     4   4   1   1
  HTRA1 WILD-TYPE 151 257  42  17
D87V4, multiclass
    clus
vv   HTRA1 MUTATED HTRA1 WILD-TYPE
  T1             4             151
  T2             4             257
  T3             1              42
  T4             1              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
  HTRA1 MUTATED     5   3     2
  HTRA1 WILD-TYPE 302  86    70
D87V5, multiclass
       clus
vv      HTRA1 MUTATED HTRA1 WILD-TYPE
  N0                5             302
  N1                3              86
  N2+N3             2              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V6, binary
                 cls
clus                0   1
  HTRA1 MUTATED     7   1
  HTRA1 WILD-TYPE 321  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      7    1
  HTRA1 WILD-TYPE  321   22
   clus
vv  HTRA1 MUTATED HTRA1 WILD-TYPE
  0             7             321
  1             1              22
[1] 2 2
[1] FALSE
D87V7, binary
                 cls
clus                0   1
  HTRA1 MUTATED     3   7
  HTRA1 WILD-TYPE 256 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      3    7
  HTRA1 WILD-TYPE  256  214
        clus
vv       HTRA1 MUTATED HTRA1 WILD-TYPE
  FEMALE             3             256
  MALE               7             214
[1] 2 2
[1] FALSE
D87V8, binary
                 cls
clus                0   1
  HTRA1 MUTATED     8   1
  HTRA1 WILD-TYPE 325  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      8    1
  HTRA1 WILD-TYPE  325   48
     clus
vv    HTRA1 MUTATED HTRA1 WILD-TYPE
  NO              8             325
  YES             1              48
[1] 2 2
[1] FALSE
D87V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HTRA1 MUTATED                            0                                 2
  HTRA1 WILD-TYPE                         18                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HTRA1 MUTATED                                                    8
  HTRA1 WILD-TYPE                                                287
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  HTRA1 MUTATED                                            0
  HTRA1 WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  HTRA1 MUTATED                                               0
  HTRA1 WILD-TYPE                                            19
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  HTRA1 MUTATED                                0
  HTRA1 WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  HTRA1 MUTATED                                    0
  HTRA1 WILD-TYPE                                  3
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  HTRA1 MUTATED                              0                             0
  HTRA1 WILD-TYPE                            2                            22
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  HTRA1 MUTATED                                               0
  HTRA1 WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  HTRA1 MUTATED                              0
  HTRA1 WILD-TYPE                            9
D87V10, multiclass
                                                    clus
vv                                                   HTRA1 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              2
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             8
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  0
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   HTRA1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   19
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V11, continuous
D87V12, continuous
                 vv
clus               R0  R1  R2  RX
  HTRA1 MUTATED     7   0   0   1
  HTRA1 WILD-TYPE 303  11   4  24
D87V13, multiclass
    clus
vv   HTRA1 MUTATED HTRA1 WILD-TYPE
  R0             7             303
  R1             0              11
  R2             0               4
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HTRA1 MUTATED                                  0     0
  HTRA1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HTRA1 MUTATED                           1     7
  HTRA1 WILD-TYPE                        28   370
D87V14, multiclass
                                  clus
vv                                 HTRA1 MUTATED HTRA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              28
  WHITE                                        7             370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V15, binary
                 cls
clus                0   1
  HTRA1 MUTATED     0   6
  HTRA1 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      0    6
  HTRA1 WILD-TYPE    6  343
                        clus
vv                       HTRA1 MUTATED HTRA1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             343
[1] 2 2
[1] FALSE

Clustering(88) Variable = ADAMTS2 MUTATION ANALYSIS
D88V1, survival
                   sevent
clus2                 0   1
  ADAMTS2 MUTATED    30   7
  ADAMTS2 WILD-TYPE 272 148
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
               37               420 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
                7               148 
$`ADAMTS2 MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4427 TCGA-44-4112 
       19.96        37.02         0.00        24.03        26.01        26.56 
TCGA-44-6777 TCGA-44-A47F TCGA-50-6593 TCGA-55-6642 TCGA-55-7227 TCGA-55-7281 
       32.45        11.08        11.05        32.65         1.74         0.59 
TCGA-55-7995 TCGA-55-8089 TCGA-55-8207 TCGA-55-8506 TCGA-55-8616 TCGA-55-A492 
        0.16         3.29         2.17         0.36         1.58        19.59 
TCGA-55-A4DG TCGA-64-1676 TCGA-69-7980 TCGA-78-7155 TCGA-83-5908 TCGA-86-7713 
       19.99        56.81        12.56        38.50        27.09        38.04 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-A456 TCGA-91-6831 TCGA-93-8067 
       35.24         4.57        24.33        29.46        10.19         6.12 
TCGA-95-7039 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A444 TCGA-NJ-A4YF TCGA-NJ-A4YI 
       41.82        17.75        23.80        10.09        71.05         0.13 
TCGA-NJ-A4YQ 
       29.13 

$`ADAMTS2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 
       50.07         3.98        14.01        45.01         9.96        47.05 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
        8.02        19.00        20.05         2.99        14.96         9.01 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       22.03         9.04         2.04         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       11.64        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       44.42        38.10        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       33.73        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
        3.25         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       11.64        22.26        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       23.05        48.62         2.86         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       40.54       107.21        70.26         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15        19.82        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.08         1.51        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
        0.10         4.80         6.64        17.62         0.49         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 
       20.58         0.92        15.81        20.19         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        20.65        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       18.84        14.04        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41         2.93        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       17.16         2.01         6.90        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        10.55       110.50        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
       31.13        34.39        20.55        32.78        19.89        37.74 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.08         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 
       27.58         0.62        28.34        26.50        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62        41.36         1.97         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45        21.57        24.30        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       19.00        14.30         6.35        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       62.60         1.64         0.26         0.43        19.82        59.11 

  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
             0.00              0.07 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
            71.05            238.29 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
            19.96             19.79 
[1] "0.0 - 71.0 (20.0)"  "0.1 - 238.3 (19.8)"
[1] "hr=" "1.4"
D88V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ADAMTS2 MUTATED         1       13       13         1         6          4
  ADAMTS2 WILD-TYPE       3      110      119        46        60         66
                   vv
clus                STAGE IIIB STAGE IV
  ADAMTS2 MUTATED            1        0
  ADAMTS2 WILD-TYPE         10       25
D88V3, multiclass
            clus
vv           ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                13               110
  STAGE IB                13               119
  STAGE IIA                1                46
  STAGE IIB                6                60
  STAGE IIIA               4                66
  STAGE IIIB               1                10
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ADAMTS2 MUTATED    15  18   4   2
  ADAMTS2 WILD-TYPE 140 243  39  16
D88V4, multiclass
    clus
vv   ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  T1              15               140
  T2              18               243
  T3               4                39
  T4               2                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
  ADAMTS2 MUTATED    31   4     3
  ADAMTS2 WILD-TYPE 276  85    69
D88V5, multiclass
       clus
vv      ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  N0                 31               276
  N1                  4                85
  N2+N3               3                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V6, binary
                   cls
clus                  0   1
  ADAMTS2 MUTATED    27   0
  ADAMTS2 WILD-TYPE 301  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED     27    0
  ADAMTS2 WILD-TYPE  301   23
   clus
vv  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  0              27               301
  1               0                23
[1] 2 2
[1] FALSE
D88V7, binary
                   cls
clus                  0   1
  ADAMTS2 MUTATED    22  17
  ADAMTS2 WILD-TYPE 237 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED     22   17
  ADAMTS2 WILD-TYPE  237  204
        clus
vv       ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  FEMALE              22               237
  MALE                17               204
[1] 2 2
[1] FALSE
D88V8, binary
                   cls
clus                  0   1
  ADAMTS2 MUTATED    20   4
  ADAMTS2 WILD-TYPE 313  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED     20    4
  ADAMTS2 WILD-TYPE  313   45
     clus
vv    ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  NO               20               313
  YES               4                45
[1] 2 2
[1] FALSE
D88V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ADAMTS2 MUTATED                            1
  ADAMTS2 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ADAMTS2 MUTATED                                  10
  ADAMTS2 WILD-TYPE                                91
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ADAMTS2 MUTATED                                                   25
  ADAMTS2 WILD-TYPE                                                270
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  ADAMTS2 MUTATED                                            0
  ADAMTS2 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  ADAMTS2 MUTATED                                               1
  ADAMTS2 WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  ADAMTS2 MUTATED                                0
  ADAMTS2 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  ADAMTS2 MUTATED                                    0
  ADAMTS2 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  ADAMTS2 MUTATED                              0                             2
  ADAMTS2 WILD-TYPE                            2                            20
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  ADAMTS2 MUTATED                                               0
  ADAMTS2 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  ADAMTS2 MUTATED                              0
  ADAMTS2 WILD-TYPE                            9
D88V10, multiclass
                                                    clus
vv                                                   ADAMTS2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              25
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   ADAMTS2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 91
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               270
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V11, continuous
D88V12, continuous
                   vv
clus                 R0  R1  R2  RX
  ADAMTS2 MUTATED    26   0   0   3
  ADAMTS2 WILD-TYPE 284  11   4  22
D88V13, multiclass
    clus
vv   ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  R0              26               284
  R1               0                11
  R2               0                 4
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAMTS2 MUTATED                                  0     2
  ADAMTS2 WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ADAMTS2 MUTATED                           1    29
  ADAMTS2 WILD-TYPE                        28   348
D88V14, multiclass
                                  clus
vv                                 ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                      1                28
  WHITE                                         29               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V15, binary
                   cls
clus                  0   1
  ADAMTS2 MUTATED     0  27
  ADAMTS2 WILD-TYPE   6 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED      0   27
  ADAMTS2 WILD-TYPE    6  322
                        clus
vv                       ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              27               322
[1] 2 2
[1] FALSE

Clustering(89) Variable = TAF1L MUTATION ANALYSIS
D89V1, survival
                 sevent
clus2               0   1
  TAF1L MUTATED    31  16
  TAF1L WILD-TYPE 271 139
  TAF1L MUTATED TAF1L WILD-TYPE 
             47             410 
  TAF1L MUTATED TAF1L WILD-TYPE 
             16             139 
$`TAF1L MUTATED`
TCGA-05-4384 TCGA-05-4396 TCGA-35-4122 TCGA-38-4631 TCGA-44-2656 TCGA-44-2657 
       14.01         9.96         7.40        11.64        46.98        44.42 
TCGA-44-5643 TCGA-44-7662 TCGA-44-8119 TCGA-44-A479 TCGA-50-5049 TCGA-50-6590 
       33.30         7.17         3.25        15.98        70.55        42.35 
TCGA-50-6593 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-6972 TCGA-55-7281 
       11.05        30.54        35.21        23.05        48.49         0.59 
TCGA-55-7995 TCGA-55-8301 TCGA-55-8621 TCGA-55-A4DF TCGA-64-5778 TCGA-69-7980 
        0.16         1.45        16.93        20.19        42.90        12.56 
TCGA-69-A59K TCGA-78-7145 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 
       17.16        27.16       129.53        21.90        39.95        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7166 TCGA-78-7167 TCGA-78-7536 TCGA-83-5908 
       32.09         5.88         8.48        88.14         8.02        27.09 
TCGA-86-6851 TCGA-86-7701 TCGA-86-A456 TCGA-91-A4BC TCGA-97-7937 TCGA-99-8032 
        5.88        31.13        29.46         1.45         5.95         1.45 
TCGA-L9-A444 TCGA-MN-A4N4 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55R 
       10.09        38.63        71.05        29.13        19.82 

$`TAF1L WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        44.61        14.73        26.30         4.37 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 
       61.28        16.44        22.72        19.46        12.03        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       18.87        29.00        29.23        13.74        12.66         8.55 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.09         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12         9.37        29.03        25.12        22.55 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        25.55        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
       10.13        36.99         7.59        27.25        34.29        13.94 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         1.74         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        1.12         0.79         1.78         1.45        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15        19.82        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.58         1.61         2.17        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       20.65        81.80        38.37        87.98         2.04        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       51.25        28.47        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
       14.01        13.45         4.24         2.01         6.90        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 
        9.24         1.25        39.09        50.33       163.10         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 
       19.27        20.58       119.51        19.50        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 
        9.57       104.19       238.29        26.53        31.20        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-7711 TCGA-86-7713 
       77.59        10.55       110.50        12.36        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF 
       30.84        27.58         0.62        28.34        26.50        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       31.69        64.60        63.52        43.79        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       24.56        34.85        36.76        21.57        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       19.13        73.91        62.60         0.13         1.64         0.26 
TCGA-NJ-A55O TCGA-O1-A52J 
        0.43        59.11 

  TAF1L MUTATED TAF1L WILD-TYPE 
           0.16            0.00 
  TAF1L MUTATED TAF1L WILD-TYPE 
         129.53          238.29 
  TAF1L MUTATED TAF1L WILD-TYPE 
         20.190          19.745 
[1] "0.2 - 129.5 (20.2)" "0.0 - 238.3 (19.7)"
[1] "hr=" "1.1"
D89V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TAF1L MUTATED         1       15       14         4         4          5
  TAF1L WILD-TYPE       3      108      118        43        62         65
                 vv
clus              STAGE IIIB STAGE IV
  TAF1L MUTATED            3        4
  TAF1L WILD-TYPE          8       21
D89V3, multiclass
            clus
vv           TAF1L MUTATED TAF1L WILD-TYPE
  STAGE I                1               3
  STAGE IA              15             108
  STAGE IB              14             118
  STAGE IIA              4              43
  STAGE IIB              4              62
  STAGE IIIA             5              65
  STAGE IIIB             3               8
  STAGE IV               4              21
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAF1L MUTATED    17  25   3   5
  TAF1L WILD-TYPE 138 236  40  13
D89V4, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  T1            17             138
  T2            25             236
  T3             3              40
  T4             5              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
  TAF1L MUTATED    35   8     6
  TAF1L WILD-TYPE 272  81    66
D89V5, multiclass
       clus
vv      TAF1L MUTATED TAF1L WILD-TYPE
  N0               35             272
  N1                8              81
  N2+N3             6              66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V6, binary
                 cls
clus                0   1
  TAF1L MUTATED    35   4
  TAF1L WILD-TYPE 293  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     35    4
  TAF1L WILD-TYPE  293   19
   clus
vv  TAF1L MUTATED TAF1L WILD-TYPE
  0            35             293
  1             4              19
[1] 2 2
[1] FALSE
D89V7, binary
                 cls
clus                0   1
  TAF1L MUTATED    21  29
  TAF1L WILD-TYPE 238 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     21   29
  TAF1L WILD-TYPE  238  192
        clus
vv       TAF1L MUTATED TAF1L WILD-TYPE
  FEMALE            21             238
  MALE              29             192
[1] 2 2
[1] FALSE
D89V8, binary
                 cls
clus                0   1
  TAF1L MUTATED    31   7
  TAF1L WILD-TYPE 302  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     31    7
  TAF1L WILD-TYPE  302   42
     clus
vv    TAF1L MUTATED TAF1L WILD-TYPE
  NO             31             302
  YES             7              42
[1] 2 2
[1] FALSE
D89V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TAF1L MUTATED                            1                                11
  TAF1L WILD-TYPE                         17                                90
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TAF1L MUTATED                                                   32
  TAF1L WILD-TYPE                                                263
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  TAF1L MUTATED                                            0
  TAF1L WILD-TYPE                                          4
                 vv
clus              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  TAF1L MUTATED                                               1
  TAF1L WILD-TYPE                                            18
                 vv
clus              LUNG CLEAR CELL ADENOCARCINOMA
  TAF1L MUTATED                                0
  TAF1L WILD-TYPE                              2
                 vv
clus              LUNG MICROPAPILLARY ADENOCARCINOMA
  TAF1L MUTATED                                    1
  TAF1L WILD-TYPE                                  2
                 vv
clus              LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  TAF1L MUTATED                              0                             4
  TAF1L WILD-TYPE                            2                            18
                 vv
clus              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  TAF1L MUTATED                                               0
  TAF1L WILD-TYPE                                             5
                 vv
clus              MUCINOUS (COLLOID) CARCINOMA
  TAF1L MUTATED                              0
  TAF1L WILD-TYPE                            9
D89V10, multiclass
                                                    clus
vv                                                   TAF1L MUTATED
  LUNG ACINAR ADENOCARCINOMA                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            32
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  1
  LUNG CLEAR CELL ADENOCARCINOMA                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                             1
  LUNG MUCINOUS ADENOCARCINOMA                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                  4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  0
  MUCINOUS (COLLOID) CARCINOMA                                   0
                                                    clus
vv                                                   TAF1L WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             263
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   18
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                   18
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    5
  MUCINOUS (COLLOID) CARCINOMA                                     9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V11, continuous
D89V12, continuous
                 vv
clus               R0  R1  R2  RX
  TAF1L MUTATED    30   2   1   4
  TAF1L WILD-TYPE 280   9   3  21
D89V13, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  R0            30             280
  R1             2               9
  R2             1               3
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF1L MUTATED                                  0     1
  TAF1L WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TAF1L MUTATED                           4    41
  TAF1L WILD-TYPE                        25   336
D89V14, multiclass
                                  clus
vv                                 TAF1L MUTATED TAF1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    4              25
  WHITE                                       41             336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V15, binary
                 cls
clus                0   1
  TAF1L MUTATED     1  34
  TAF1L WILD-TYPE   5 315
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED      1   34
  TAF1L WILD-TYPE    5  315
                        clus
vv                       TAF1L MUTATED TAF1L WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            34             315
[1] 2 2
[1] FALSE

Clustering(90) Variable = PLEKHB2 MUTATION ANALYSIS
D90V1, survival
                   sevent
clus2                 0   1
  PLEKHB2 MUTATED     4   2
  PLEKHB2 WILD-TYPE 298 153
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               451 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                2               153 
$`PLEKHB2 MUTATED`
TCGA-44-7662 TCGA-49-6767 TCGA-50-5941 TCGA-55-A4DF TCGA-MP-A4SV TCGA-NJ-A55R 
        7.17        22.26         9.37        20.19        86.14        19.82 

$`PLEKHB2 WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       44.61        14.73        26.30         4.37        46.98        44.42 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       38.10        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       17.16        11.64        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       40.60        78.67        21.47         8.45        15.12        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       23.05        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26         1.74         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.45        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        28.47        20.05        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.01         6.90        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       50.33       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30         6.35        10.09        27.19        38.63         2.76 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-O1-A52J 
       59.11 

  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
             7.17              0.00 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
            86.14            238.29 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
           20.005            19.760 
[1] "7.2 - 86.1 (20.0)"  "0.0 - 238.3 (19.8)"
[1] "hr=" "1.1"
D90V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  PLEKHB2 MUTATED         0        2        2         0         1          1
  PLEKHB2 WILD-TYPE       4      121      130        47        65         69
                   vv
clus                STAGE IIIB STAGE IV
  PLEKHB2 MUTATED            0        0
  PLEKHB2 WILD-TYPE         11       25
D90V3, multiclass
            clus
vv           PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               121
  STAGE IB                 2               130
  STAGE IIA                0                47
  STAGE IIB                1                65
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                25
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHB2 MUTATED     2   3   1   0
  PLEKHB2 WILD-TYPE 153 258  42  18
D90V4, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  T1               2               153
  T2               3               258
  T3               1                42
  T4               0                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
  PLEKHB2 MUTATED     5   0     1
  PLEKHB2 WILD-TYPE 302  89    71
D90V5, multiclass
       clus
vv      PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  N0                  5               302
  N1                  0                89
  N2+N3               1                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V6, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     2   0
  PLEKHB2 WILD-TYPE 326  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      2    0
  PLEKHB2 WILD-TYPE  326   23
   clus
vv  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  0               2               326
  1               0                23
[1] 2 2
[1] FALSE
D90V7, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     2   4
  PLEKHB2 WILD-TYPE 257 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      2    4
  PLEKHB2 WILD-TYPE  257  217
        clus
vv       PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  FEMALE               2               257
  MALE                 4               217
[1] 2 2
[1] FALSE
D90V8, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     4   0
  PLEKHB2 WILD-TYPE 329  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      4    0
  PLEKHB2 WILD-TYPE  329   49
     clus
vv    PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  NO                4               329
  YES               0                49
[1] 2 2
[1] FALSE
D90V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  PLEKHB2 MUTATED                            0
  PLEKHB2 WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  PLEKHB2 MUTATED                                   0
  PLEKHB2 WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PLEKHB2 MUTATED                                                    6
  PLEKHB2 WILD-TYPE                                                289
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  PLEKHB2 MUTATED                                            0
  PLEKHB2 WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  PLEKHB2 MUTATED                                               0
  PLEKHB2 WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  PLEKHB2 MUTATED                                0
  PLEKHB2 WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  PLEKHB2 MUTATED                                    0
  PLEKHB2 WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  PLEKHB2 MUTATED                              0                             0
  PLEKHB2 WILD-TYPE                            2                            22
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  PLEKHB2 MUTATED                                               0
  PLEKHB2 WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  PLEKHB2 MUTATED                              0
  PLEKHB2 WILD-TYPE                            9
D90V10, multiclass
                                                    clus
vv                                                   PLEKHB2 MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               6
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   PLEKHB2 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V11, continuous
D90V12, continuous
[1] "Remove cluster labels:" "PLEKHB2 MUTATED"       
clus
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                2               255 
       TCGA-05-4384        TCGA-05-4390        TCGA-05-4396        TCGA-05-4405 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-05-4410        TCGA-05-4415        TCGA-05-4417        TCGA-05-4424 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-05-4427        TCGA-05-4433        TCGA-05-5420        TCGA-05-5423 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-05-5425        TCGA-05-5428        TCGA-35-4122        TCGA-35-4123 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-35-5375        TCGA-38-4625        TCGA-38-4626        TCGA-38-7271 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-38-A44F        TCGA-44-2656        TCGA-44-2657        TCGA-44-3396 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-3398        TCGA-44-3918        TCGA-44-4112        TCGA-44-5644 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-5645        TCGA-44-6144        TCGA-44-6145        TCGA-44-6147 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-6148        TCGA-44-6774        TCGA-44-6775        TCGA-44-6776 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-6777        TCGA-44-6778        TCGA-44-6779        TCGA-44-7659 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-7660        TCGA-44-7661        TCGA-44-7667        TCGA-44-7669 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-7670        TCGA-44-7672        TCGA-44-8117        TCGA-44-8119 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-8120        TCGA-44-A479        TCGA-44-A47A        TCGA-44-A47B 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-A47F        TCGA-44-A47G        TCGA-44-A4SS        TCGA-44-A4SU 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-49-4486        TCGA-49-4494        TCGA-49-4505        TCGA-53-7624 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-53-7626        TCGA-53-7813        TCGA-53-A4EZ        TCGA-55-1592 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-1595        TCGA-55-5899        TCGA-55-6642        TCGA-55-6712 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-6971        TCGA-55-7227        TCGA-55-7283        TCGA-55-7570 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-7574        TCGA-55-7576        TCGA-55-7724        TCGA-55-7725 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-7726        TCGA-55-7728        TCGA-55-7907        TCGA-55-7910 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-7911        TCGA-55-7914        TCGA-55-8089        TCGA-55-8092 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-8094        TCGA-55-8096        TCGA-55-8097        TCGA-55-8205 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-8299        TCGA-55-8301        TCGA-55-8302        TCGA-55-8506 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-8507        TCGA-55-8511        TCGA-55-8512        TCGA-55-8514 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-8615        TCGA-55-8620        TCGA-55-8621        TCGA-55-A48X 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-A48Y        TCGA-55-A48Z        TCGA-55-A490        TCGA-55-A491 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-A492        TCGA-55-A493        TCGA-55-A494        TCGA-62-8398 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-64-1677        TCGA-64-1681        TCGA-64-5774        TCGA-64-5775 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-64-5778        TCGA-64-5779        TCGA-64-5781        TCGA-69-7761 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-69-7763        TCGA-69-7764        TCGA-69-7765        TCGA-69-7974 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-69-7979        TCGA-69-8253        TCGA-69-8255        TCGA-69-A59K 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-73-4659        TCGA-73-4662        TCGA-73-4666        TCGA-73-4668 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-73-4670        TCGA-73-4675        TCGA-73-4676        TCGA-73-7498 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-75-6214        TCGA-75-7025        TCGA-75-7027        TCGA-75-7031 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7145        TCGA-78-7146        TCGA-78-7147        TCGA-78-7148 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7149        TCGA-78-7150        TCGA-78-7152        TCGA-78-7153 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7154        TCGA-78-7155        TCGA-78-7156        TCGA-78-7158 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7159        TCGA-78-7160        TCGA-78-7161        TCGA-78-7162 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7163        TCGA-78-7166        TCGA-78-7167        TCGA-78-7220 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7535        TCGA-78-7536        TCGA-78-7537        TCGA-78-7539 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7542        TCGA-78-7633        TCGA-78-8640        TCGA-78-8648 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-8655        TCGA-78-8660        TCGA-78-8662        TCGA-80-5607 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-80-5608        TCGA-83-5908        TCGA-86-6851        TCGA-86-7711 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7954        TCGA-86-8054        TCGA-86-8055 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-86-8056        TCGA-86-8073        TCGA-86-8074        TCGA-86-8281 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8359        TCGA-86-8669        TCGA-86-8673 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-86-8674        TCGA-86-A456        TCGA-91-6829        TCGA-91-6830 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-91-6836        TCGA-91-6840        TCGA-91-6849        TCGA-91-8499 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-91-A4BC        TCGA-93-7347        TCGA-93-7348        TCGA-93-8067 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-93-A4JQ        TCGA-95-7043 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-95-7562        TCGA-95-7567        TCGA-95-7944        TCGA-95-7947 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-95-7948        TCGA-95-A4VK        TCGA-95-A4VN        TCGA-95-A4VP 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-97-7546        TCGA-97-7553        TCGA-97-7554        TCGA-97-7941 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-97-8171        TCGA-97-8172        TCGA-97-8174        TCGA-97-8176 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-97-8179        TCGA-97-A4LX        TCGA-97-A4M0        TCGA-97-A4M1 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-97-A4M2        TCGA-97-A4M3        TCGA-97-A4M5        TCGA-97-A4M7 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-99-7458        TCGA-99-8025        TCGA-99-8028        TCGA-99-8032 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-J2-8194        TCGA-J2-A4AD        TCGA-J2-A4AG        TCGA-L4-A4E5 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-L4-A4E6        TCGA-L9-A443        TCGA-L9-A444        TCGA-MN-A4N1 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-MN-A4N4        TCGA-MN-A4N5        TCGA-MP-A4SW        TCGA-MP-A4T2 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-MP-A4T4        TCGA-MP-A4T7        TCGA-MP-A4T8        TCGA-MP-A4T9 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-MP-A4TA        TCGA-MP-A4TC        TCGA-MP-A4TE        TCGA-MP-A4TF 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-MP-A4TH        TCGA-MP-A4TI        TCGA-MP-A4TK        TCGA-MP-A5C7 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-NJ-A4YG        TCGA-NJ-A4YI        TCGA-O1-A52J 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  PLEKHB2 MUTATED     3   0   0   0
  PLEKHB2 WILD-TYPE 307  11   4  25
D90V13, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  R0               3               307
  R1               0                11
  R2               0                 4
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHB2 MUTATED                                  0     0
  PLEKHB2 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHB2 MUTATED                           0     5
  PLEKHB2 WILD-TYPE                        29   372
D90V14, multiclass
                                  clus
vv                                 PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                29
  WHITE                                          5               372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V15, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     0   3
  PLEKHB2 WILD-TYPE   6 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      0    3
  PLEKHB2 WILD-TYPE    6  346
                        clus
vv                       PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               3               346
[1] 2 2
[1] FALSE
